python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/0.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.0.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/100.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.100.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/101.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.101.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/102.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.102.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/103.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.103.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/104.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.104.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/105.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.105.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/106.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.106.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/107.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.107.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/108.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.108.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/109.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.109.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/10.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.10.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/110.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.110.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/111.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.111.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/112.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.112.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/113.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.113.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/114.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.114.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/115.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.115.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/116.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.116.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/117.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.117.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/118.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.118.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/119.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.119.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/11.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.11.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/120.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.120.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/121.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.121.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/122.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.122.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/123.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.123.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/124.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.124.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/125.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.125.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/126.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.126.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/127.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.127.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/128.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.128.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/129.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.129.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/12.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.12.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/130.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.130.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/131.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.131.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/132.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.132.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/133.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.133.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/134.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.134.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/135.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.135.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/136.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.136.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/137.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.137.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/138.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.138.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/139.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.139.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/13.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.13.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/140.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.140.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/141.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.141.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/142.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.142.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/143.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.143.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/144.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.144.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/145.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.145.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/146.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.146.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/147.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.147.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/148.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.148.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/149.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.149.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/14.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.14.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/150.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.150.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/151.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.151.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/152.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.152.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/153.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.153.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/154.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.154.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/155.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.155.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/156.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.156.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/157.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.157.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/158.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.158.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/159.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.159.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/15.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.15.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/160.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.160.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/161.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.161.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/162.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.162.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/163.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.163.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/164.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.164.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/165.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.165.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/166.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.166.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/167.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.167.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/168.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.168.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/169.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.169.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/16.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.16.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/170.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.170.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/171.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.171.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/172.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.172.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/173.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.173.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/174.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.174.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/175.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.175.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/176.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.176.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/177.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.177.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/178.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.178.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/179.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.179.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/17.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.17.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/180.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.180.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/181.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.181.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/182.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.182.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/183.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.183.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/184.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.184.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/185.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.185.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/186.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.186.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/187.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.187.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/188.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.188.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/189.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.189.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/18.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.18.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/190.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.190.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/191.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.191.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/192.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.192.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/193.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.193.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/194.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.194.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/195.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.195.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/196.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.196.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/197.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.197.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/198.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.198.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/199.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.199.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/19.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.19.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/1.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.1.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/200.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.200.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/201.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.201.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/202.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.202.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/203.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.203.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/204.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.204.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/205.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.205.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/206.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.206.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/207.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.207.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/208.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.208.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/209.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.209.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/20.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.20.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/210.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.210.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/211.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.211.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/212.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.212.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/213.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.213.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/214.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.214.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/215.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.215.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/216.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.216.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/217.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.217.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/218.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.218.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/219.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.219.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/21.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.21.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/220.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.220.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/221.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.221.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/222.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.222.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/223.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.223.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/224.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.224.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/225.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.225.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/226.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.226.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/227.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.227.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/228.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.228.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/229.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.229.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/22.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.22.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/230.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.230.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/231.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.231.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/232.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.232.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/233.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.233.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/234.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.234.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/235.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.235.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/236.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.236.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/237.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.237.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/238.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.238.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/239.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.239.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/23.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.23.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/240.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.240.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/241.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.241.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/242.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.242.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/243.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.243.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/244.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.244.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/245.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.245.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/246.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.246.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/247.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.247.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/248.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.248.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/249.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.249.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/24.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.24.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/250.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.250.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/251.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.251.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/252.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.252.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/253.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.253.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/254.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.254.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/255.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.255.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/256.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.256.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/257.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.257.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/258.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.258.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/259.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.259.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/25.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.25.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/260.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.260.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/261.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.261.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/262.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.262.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/263.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.263.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/264.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.264.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/265.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.265.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/266.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.266.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/267.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.267.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/268.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.268.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/269.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.269.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/26.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.26.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/270.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.270.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/271.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.271.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/272.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.272.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/273.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.273.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/274.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.274.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/275.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.275.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/276.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.276.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/277.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.277.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/278.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.278.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/279.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.279.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/27.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.27.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/280.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.280.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/281.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.281.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/282.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.282.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/283.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.283.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/284.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.284.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/285.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.285.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/286.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.286.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/287.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.287.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/288.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.288.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/289.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.289.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/28.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.28.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/290.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.290.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/291.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.291.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/292.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.292.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/293.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.293.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/294.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.294.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/295.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.295.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/296.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.296.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/297.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.297.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/298.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.298.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/299.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.299.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/29.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.29.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/2.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.2.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/300.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.300.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/301.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.301.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/302.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.302.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/303.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.303.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/304.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.304.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/305.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.305.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/306.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.306.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/307.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.307.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/308.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.308.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/309.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.309.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/30.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.30.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/310.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.310.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/311.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.311.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/312.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.312.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/313.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.313.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/314.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.314.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/315.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.315.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/316.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.316.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/317.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.317.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/318.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.318.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/319.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.319.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/31.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.31.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/320.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.320.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/321.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.321.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/322.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.322.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/323.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.323.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/324.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.324.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/325.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.325.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/326.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.326.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/327.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.327.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/328.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.328.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/329.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.329.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/32.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.32.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/330.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.330.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/331.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.331.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/332.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.332.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/333.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.333.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/334.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.334.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/335.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.335.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/336.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.336.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/337.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.337.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/338.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.338.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/339.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.339.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/33.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.33.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/340.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.340.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/341.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.341.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/342.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.342.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/343.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.343.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/344.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.344.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/345.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.345.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/346.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.346.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/347.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.347.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/348.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.348.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/349.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.349.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/34.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.34.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/350.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.350.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/351.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.351.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/352.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.352.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/353.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.353.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/354.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.354.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/355.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.355.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/356.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.356.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/357.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.357.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/358.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.358.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/359.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.359.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/35.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.35.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/360.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.360.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/361.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.361.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/362.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.362.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/363.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.363.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/364.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.364.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/365.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.365.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/366.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.366.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/367.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.367.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/368.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.368.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/369.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.369.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/36.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.36.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/370.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.370.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/371.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.371.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/372.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.372.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/373.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.373.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/374.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.374.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/375.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.375.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/376.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.376.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/377.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.377.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/378.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.378.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/379.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.379.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/37.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.37.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/380.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.380.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/381.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.381.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/382.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.382.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/383.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.383.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/384.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.384.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/385.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.385.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/386.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.386.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/387.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.387.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/388.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.388.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/389.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.389.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/38.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.38.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/390.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.390.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/391.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.391.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/392.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.392.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/393.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.393.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/394.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.394.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/395.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.395.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/396.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.396.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/397.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.397.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/398.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.398.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/399.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.399.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/39.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.39.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/3.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.3.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/400.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.400.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/401.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.401.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/402.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.402.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/403.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.403.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/404.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.404.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/405.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.405.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/406.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.406.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/407.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.407.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/408.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.408.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/409.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.409.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/40.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.40.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/410.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.410.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/411.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.411.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/412.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.412.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/413.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.413.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/414.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.414.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/415.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.415.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/416.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.416.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/417.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.417.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/418.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.418.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/419.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.419.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/41.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.41.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/420.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.420.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/421.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.421.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/422.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.422.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/423.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.423.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/424.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.424.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/425.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.425.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/426.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.426.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/427.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.427.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/428.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.428.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/429.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.429.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/42.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.42.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/430.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.430.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/431.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.431.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/432.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.432.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/433.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.433.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/434.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.434.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/435.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.435.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/436.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.436.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/437.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.437.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/438.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.438.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/439.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.439.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/43.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.43.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/440.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.440.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/441.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.441.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/442.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.442.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/443.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.443.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/444.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.444.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/445.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.445.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/446.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.446.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/447.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.447.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/448.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.448.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/449.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.449.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/44.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.44.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/450.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.450.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/451.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.451.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/452.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.452.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/453.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.453.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/454.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.454.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/455.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.455.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/456.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.456.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/457.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.457.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/458.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.458.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/459.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.459.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/45.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.45.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/460.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.460.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/461.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.461.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/462.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.462.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/463.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.463.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/464.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.464.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/465.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.465.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/466.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.466.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/467.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.467.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/468.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.468.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/469.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.469.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/46.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.46.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/470.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.470.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/471.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.471.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/472.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.472.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/473.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.473.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/474.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.474.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/475.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.475.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/476.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.476.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/477.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.477.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/478.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.478.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/479.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.479.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/47.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.47.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/480.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.480.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/481.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.481.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/482.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.482.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/483.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.483.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/484.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.484.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/485.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.485.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/486.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.486.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/487.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.487.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/488.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.488.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/489.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.489.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/48.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.48.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/490.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.490.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/491.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.491.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/492.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.492.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/493.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.493.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/494.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.494.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/495.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.495.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/496.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.496.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/497.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.497.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/498.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.498.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/499.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.499.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/49.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.49.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/4.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.4.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/500.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.500.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/501.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.501.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/502.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.502.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/503.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.503.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/504.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.504.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/505.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.505.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/506.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.506.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/507.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.507.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/508.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.508.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/509.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.509.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/50.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.50.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/510.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.510.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/511.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.511.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/512.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.512.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/513.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.513.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/514.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.514.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/515.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.515.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/516.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.516.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/517.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.517.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/518.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.518.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/519.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.519.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/51.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.51.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/520.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.520.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/521.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.521.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/522.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.522.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/523.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.523.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/524.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.524.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/525.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.525.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/526.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.526.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/527.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.527.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/528.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.528.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/529.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.529.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/52.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.52.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/530.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.530.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/531.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.531.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/532.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.532.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/533.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.533.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/534.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.534.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/535.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.535.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/536.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.536.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/537.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.537.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/538.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.538.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/539.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.539.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/53.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.53.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/540.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.540.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/541.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.541.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/542.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.542.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/543.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.543.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/544.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.544.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/545.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.545.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/546.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.546.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/547.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.547.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/548.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.548.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/549.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.549.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/54.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.54.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/550.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.550.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/551.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.551.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/552.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.552.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/553.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.553.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/554.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.554.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/555.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.555.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/556.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.556.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/557.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.557.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/558.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.558.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/559.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.559.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/55.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.55.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/560.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.560.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/561.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.561.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/562.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.562.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/563.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.563.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/564.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.564.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/565.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.565.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/566.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.566.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/567.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.567.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/568.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.568.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/569.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.569.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/56.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.56.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/570.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.570.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/571.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.571.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/572.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.572.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/573.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.573.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/574.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.574.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/575.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.575.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/576.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.576.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/577.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.577.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/578.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.578.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/579.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.579.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/57.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.57.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/580.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.580.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/581.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.581.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/582.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.582.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/583.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.583.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/584.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.584.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/585.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.585.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/586.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.586.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/587.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.587.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/588.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.588.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/589.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.589.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/58.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.58.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/590.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.590.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/591.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.591.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/592.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.592.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/593.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.593.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/594.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.594.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/595.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.595.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/596.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.596.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/597.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.597.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/598.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.598.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/599.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.599.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/59.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.59.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/5.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.5.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/600.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.600.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/601.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.601.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/602.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.602.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/603.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.603.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/604.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.604.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/605.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.605.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/606.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.606.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/607.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.607.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/608.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.608.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/609.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.609.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/60.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.60.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/610.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.610.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/611.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.611.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/612.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.612.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/613.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.613.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/614.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.614.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/615.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.615.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/616.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.616.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/617.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.617.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/618.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.618.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/619.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.619.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/61.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.61.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/620.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.620.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/621.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.621.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/622.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.622.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/623.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.623.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/624.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.624.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/625.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.625.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/626.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.626.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/627.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.627.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/628.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.628.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/629.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.629.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/62.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.62.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/630.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.630.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/631.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.631.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/632.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.632.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/633.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.633.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/634.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.634.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/635.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.635.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/636.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.636.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/637.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.637.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/638.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.638.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/639.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.639.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/63.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.63.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/640.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.640.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/641.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.641.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/642.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.642.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/643.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.643.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/644.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.644.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/645.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.645.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/64.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.64.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/65.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.65.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/66.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.66.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/67.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.67.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/68.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.68.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/69.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.69.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/6.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.6.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/70.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.70.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/71.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.71.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/72.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.72.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/73.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.73.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/74.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.74.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/75.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.75.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/76.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.76.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/77.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.77.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/78.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.78.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/79.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.79.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/7.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.7.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/80.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.80.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/81.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.81.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/82.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.82.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/83.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.83.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/84.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.84.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/85.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.85.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/86.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.86.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/87.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.87.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/88.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.88.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/89.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.89.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/8.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.8.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/90.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.90.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/91.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.91.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/92.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.92.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/93.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.93.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/94.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.94.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/95.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.95.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/96.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.96.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/97.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.97.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/98.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.98.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/99.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.99.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/9.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.9.tombo.m6A-only -m6A-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/0.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.0.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/100.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.100.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/101.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.101.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/102.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.102.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/103.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.103.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/104.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.104.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/105.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.105.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/106.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.106.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/107.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.107.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/108.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.108.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/109.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.109.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/10.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.10.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/110.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.110.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/111.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.111.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/112.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.112.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/113.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.113.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/114.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.114.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/115.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.115.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/116.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.116.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/117.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.117.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/118.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.118.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/119.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.119.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/11.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.11.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/120.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.120.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/121.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.121.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/122.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.122.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/123.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.123.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/124.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.124.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/125.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.125.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/126.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.126.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/127.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.127.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/128.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.128.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/129.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.129.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/12.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.12.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/130.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.130.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/131.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.131.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/132.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.132.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/133.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.133.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/134.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.134.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/135.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.135.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/136.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.136.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/137.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.137.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/138.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.138.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/139.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.139.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/13.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.13.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/140.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.140.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/141.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.141.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/142.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.142.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/143.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.143.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/144.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.144.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/145.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.145.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/146.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.146.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/147.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.147.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/148.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.148.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/149.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.149.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/14.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.14.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/150.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.150.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/151.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.151.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/152.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.152.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/153.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.153.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/154.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.154.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/155.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.155.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/156.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.156.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/157.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.157.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/158.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.158.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/159.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.159.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/15.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.15.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/160.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.160.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/161.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.161.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/162.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.162.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/163.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.163.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/164.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.164.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/165.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.165.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/166.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.166.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/167.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.167.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/168.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.168.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/169.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.169.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/16.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.16.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/170.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.170.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/171.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.171.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/172.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.172.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/173.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.173.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/174.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.174.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/175.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.175.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/176.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.176.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/177.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.177.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/178.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.178.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/179.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.179.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/17.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.17.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/180.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.180.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/181.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.181.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/182.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.182.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/183.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.183.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/184.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.184.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/185.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.185.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/186.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.186.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/187.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.187.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/188.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.188.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/189.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.189.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/18.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.18.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/190.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.190.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/191.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.191.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/192.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.192.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/193.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.193.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/194.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.194.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/195.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.195.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/196.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.196.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/197.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.197.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/198.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.198.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/199.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.199.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/19.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.19.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/1.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.1.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/200.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.200.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/201.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.201.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/202.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.202.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/203.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.203.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/204.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.204.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/205.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.205.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/206.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.206.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/207.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.207.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/208.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.208.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/209.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.209.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/20.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.20.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/210.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.210.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/211.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.211.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/212.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.212.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/213.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.213.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/214.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.214.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/215.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.215.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/216.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.216.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/217.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.217.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/218.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.218.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/219.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.219.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/21.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.21.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/220.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.220.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/221.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.221.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/222.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.222.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/223.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.223.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/224.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.224.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/225.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.225.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/226.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.226.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/227.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.227.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/228.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.228.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/229.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.229.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/22.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.22.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/230.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.230.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/231.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.231.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/232.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.232.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/233.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.233.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/234.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.234.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/235.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.235.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/236.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.236.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/237.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.237.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/238.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.238.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/239.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.239.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/23.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.23.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/240.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.240.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/241.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.241.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/242.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.242.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/243.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.243.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/244.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.244.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/245.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.245.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/246.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.246.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/247.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.247.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/248.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.248.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/249.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.249.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/24.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.24.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/250.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.250.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/251.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.251.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/252.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.252.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/253.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.253.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/254.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.254.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/255.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.255.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/256.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.256.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/257.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.257.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/258.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.258.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/259.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.259.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/25.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.25.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/260.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.260.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/261.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.261.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/262.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.262.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/263.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.263.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/264.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.264.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/265.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.265.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/266.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.266.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/267.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.267.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/268.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.268.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/269.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.269.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/26.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.26.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/270.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.270.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/271.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.271.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/272.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.272.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/273.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.273.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/274.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.274.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/275.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.275.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/276.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.276.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/277.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.277.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/278.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.278.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/279.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.279.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/27.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.27.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/280.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.280.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/281.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.281.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/282.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.282.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/283.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.283.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/284.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.284.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/285.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.285.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/286.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.286.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/287.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.287.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/288.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.288.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/289.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.289.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/28.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.28.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/290.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.290.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/291.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.291.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/292.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.292.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/293.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.293.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/294.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.294.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/295.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.295.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/296.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.296.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/297.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.297.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/298.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.298.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/299.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.299.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/29.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.29.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/2.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.2.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/300.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.300.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/301.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.301.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/302.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.302.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/303.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.303.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/304.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.304.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/305.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.305.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/306.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.306.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/307.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.307.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/308.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.308.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/309.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.309.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/30.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.30.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/310.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.310.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/311.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.311.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/312.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.312.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/313.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.313.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/314.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.314.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/315.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.315.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/316.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.316.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/317.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.317.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/318.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.318.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/319.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.319.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/31.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.31.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/320.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.320.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/321.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.321.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/322.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.322.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/323.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.323.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/324.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.324.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/325.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.325.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/326.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.326.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/327.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.327.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/328.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.328.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/329.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.329.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/32.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.32.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/330.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.330.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/331.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.331.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/332.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.332.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/333.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.333.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/334.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.334.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/335.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.335.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/336.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.336.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/337.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.337.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/338.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.338.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/339.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.339.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/33.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.33.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/340.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.340.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/341.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.341.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/342.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.342.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/343.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.343.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/344.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.344.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/345.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.345.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/346.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.346.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/347.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.347.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/348.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.348.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/349.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.349.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/34.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.34.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/350.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.350.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/351.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.351.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/352.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.352.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/353.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.353.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/354.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.354.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/355.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.355.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/356.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.356.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/357.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.357.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/358.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.358.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/359.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.359.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/35.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.35.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/360.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.360.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/361.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.361.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/362.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.362.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/363.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.363.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/364.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.364.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/365.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.365.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/366.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.366.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/367.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.367.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/368.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.368.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/369.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.369.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/36.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.36.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/370.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.370.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/371.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.371.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/372.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.372.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/373.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.373.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/374.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.374.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/375.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.375.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/376.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.376.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/377.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.377.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/378.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.378.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/379.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.379.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/37.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.37.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/380.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.380.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/381.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.381.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/382.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.382.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/383.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.383.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/384.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.384.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/385.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.385.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/386.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.386.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/387.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.387.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/388.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.388.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/389.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.389.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/38.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.38.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/390.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.390.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/391.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.391.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/392.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.392.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/393.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.393.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/394.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.394.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/395.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.395.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/396.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.396.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/397.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.397.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/398.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.398.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/399.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.399.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/39.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.39.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/3.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.3.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/400.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.400.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/401.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.401.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/402.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.402.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/403.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.403.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/404.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.404.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/405.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.405.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/406.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.406.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/407.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.407.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/408.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.408.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/409.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.409.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/40.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.40.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/410.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.410.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/411.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.411.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/412.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.412.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/413.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.413.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/414.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.414.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/415.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.415.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/416.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.416.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/417.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.417.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/418.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.418.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/419.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.419.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/41.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.41.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/420.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.420.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/421.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.421.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/422.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.422.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/423.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.423.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/424.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.424.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/425.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.425.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/426.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.426.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/427.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.427.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/428.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.428.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/429.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.429.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/42.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.42.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/430.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.430.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/431.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.431.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/432.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.432.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/433.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.433.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/434.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.434.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/435.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.435.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/436.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.436.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/437.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.437.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/438.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.438.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/439.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.439.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/43.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.43.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/440.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.440.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/441.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.441.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/442.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.442.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/443.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.443.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/444.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.444.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/445.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.445.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/446.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.446.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/447.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.447.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/448.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.448.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/449.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.449.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/44.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.44.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/450.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.450.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/451.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.451.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/452.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.452.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/453.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.453.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/454.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.454.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/455.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.455.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/456.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.456.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/457.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.457.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/458.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.458.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/459.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.459.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/45.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.45.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/460.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.460.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/461.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.461.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/462.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.462.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/463.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.463.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/464.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.464.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/465.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.465.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/466.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.466.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/467.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.467.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/468.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.468.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/469.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.469.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/46.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.46.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/470.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.470.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/471.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.471.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/472.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.472.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/473.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.473.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/474.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.474.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/475.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.475.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/476.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.476.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/477.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.477.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/478.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.478.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/479.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.479.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/47.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.47.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/480.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.480.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/481.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.481.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/482.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.482.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/483.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.483.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/484.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.484.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/485.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.485.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/486.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.486.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/487.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.487.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/488.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.488.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/489.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.489.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/48.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.48.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/490.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.490.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/491.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.491.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/492.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.492.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/493.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.493.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/494.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.494.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/495.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.495.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/496.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.496.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/497.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.497.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/498.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.498.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/499.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.499.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/49.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.49.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/4.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.4.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/500.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.500.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/501.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.501.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/502.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.502.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/503.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.503.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/504.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.504.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/505.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.505.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/506.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.506.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/507.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.507.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/508.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.508.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/509.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.509.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/50.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.50.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/510.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.510.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/511.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.511.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/512.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.512.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/513.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.513.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/514.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.514.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/515.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.515.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/516.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.516.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/517.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.517.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/518.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.518.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/519.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.519.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/51.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.51.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/520.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.520.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/521.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.521.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/522.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.522.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/523.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.523.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/524.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.524.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/525.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.525.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/526.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.526.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/527.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.527.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/528.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.528.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/529.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.529.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/52.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.52.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/530.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.530.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/531.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.531.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/532.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.532.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/533.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.533.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/534.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.534.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/535.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.535.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/536.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.536.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/537.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.537.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/538.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.538.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/539.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.539.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/53.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.53.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/540.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.540.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/541.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.541.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/542.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.542.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/543.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.543.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/544.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.544.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/545.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.545.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/546.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.546.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/547.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.547.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/548.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.548.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/549.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.549.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/54.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.54.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/550.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.550.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/551.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.551.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/552.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.552.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/553.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.553.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/554.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.554.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/555.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.555.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/556.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.556.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/557.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.557.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/558.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.558.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/559.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.559.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/55.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.55.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/560.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.560.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/561.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.561.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/562.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.562.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/563.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.563.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/564.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.564.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/565.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.565.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/566.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.566.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/567.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.567.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/568.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.568.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/569.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.569.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/56.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.56.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/570.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.570.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/571.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.571.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/572.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.572.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/573.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.573.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/574.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.574.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/575.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.575.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/576.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.576.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/577.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.577.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/578.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.578.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/579.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.579.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/57.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.57.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/580.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.580.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/581.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.581.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/582.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.582.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/583.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.583.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/584.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.584.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/585.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.585.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/586.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.586.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/587.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.587.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/588.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.588.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/589.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.589.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/58.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.58.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/590.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.590.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/591.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.591.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/592.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.592.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/593.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.593.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/594.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.594.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/595.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.595.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/596.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.596.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/597.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.597.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/598.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.598.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/599.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.599.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/59.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.59.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/5.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.5.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/600.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.600.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/601.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.601.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/602.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.602.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/603.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.603.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/604.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.604.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/605.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.605.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/606.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.606.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/607.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.607.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/608.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.608.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/609.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.609.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/60.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.60.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/610.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.610.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/611.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.611.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/612.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.612.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/613.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.613.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/614.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.614.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/615.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.615.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/616.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.616.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/617.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.617.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/618.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.618.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/619.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.619.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/61.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.61.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/620.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.620.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/621.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.621.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/622.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.622.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/623.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.623.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/624.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.624.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/625.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.625.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/626.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.626.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/627.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.627.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/628.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.628.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/629.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.629.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/62.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.62.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/630.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.630.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/631.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.631.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/632.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.632.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/633.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.633.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/634.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.634.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/635.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.635.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/636.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.636.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/637.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.637.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/638.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.638.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/639.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.639.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/63.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.63.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/640.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.640.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/641.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.641.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/642.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.642.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/643.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.643.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/644.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.644.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/645.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.645.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/64.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.64.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/65.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.65.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/66.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.66.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/67.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.67.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/68.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.68.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/69.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.69.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/6.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.6.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/70.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.70.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/71.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.71.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/72.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.72.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/73.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.73.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/74.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.74.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/75.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.75.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/76.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.76.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/77.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.77.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/78.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.78.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/79.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.79.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/7.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.7.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/80.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.80.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/81.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.81.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/82.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.82.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/83.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.83.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/84.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.84.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/85.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.85.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/86.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.86.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/87.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.87.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/88.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.88.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/89.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.89.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/8.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.8.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/90.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.90.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/91.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.91.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/92.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.92.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/93.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.93.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/94.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.94.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/95.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.95.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/96.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.96.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/97.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.97.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/98.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.98.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/99.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.99.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/9.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.9.tombo.GC-only -m5C-only -GC-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/0.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.0.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/100.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.100.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/101.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.101.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/102.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.102.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/103.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.103.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/104.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.104.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/105.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.105.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/106.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.106.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/107.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.107.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/108.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.108.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/109.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.109.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/10.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.10.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/110.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.110.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/111.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.111.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/112.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.112.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/113.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.113.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/114.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.114.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/115.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.115.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/116.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.116.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/117.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.117.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/118.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.118.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/119.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.119.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/11.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.11.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/120.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.120.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/121.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.121.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/122.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.122.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/123.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.123.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/124.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.124.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/125.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.125.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/126.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.126.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/127.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.127.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/128.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.128.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/129.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.129.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/12.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.12.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/130.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.130.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/131.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.131.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/132.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.132.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/133.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.133.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/134.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.134.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/135.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.135.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/136.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.136.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/137.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.137.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/138.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.138.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/139.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.139.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/13.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.13.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/140.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.140.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/141.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.141.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/142.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.142.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/143.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.143.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/144.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.144.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/145.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.145.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/146.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.146.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/147.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.147.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/148.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.148.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/149.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.149.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/14.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.14.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/150.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.150.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/151.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.151.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/152.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.152.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/153.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.153.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/154.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.154.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/155.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.155.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/156.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.156.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/157.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.157.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/158.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.158.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/159.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.159.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/15.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.15.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/160.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.160.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/161.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.161.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/162.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.162.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/163.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.163.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/164.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.164.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/165.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.165.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/166.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.166.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/167.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.167.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/168.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.168.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/169.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.169.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/16.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.16.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/170.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.170.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/171.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.171.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/172.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.172.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/173.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.173.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/174.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.174.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/175.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.175.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/176.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.176.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/177.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.177.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/178.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.178.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/179.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.179.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/17.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.17.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/180.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.180.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/181.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.181.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/182.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.182.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/183.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.183.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/184.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.184.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/185.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.185.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/186.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.186.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/187.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.187.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/188.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.188.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/189.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.189.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/18.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.18.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/190.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.190.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/191.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.191.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/192.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.192.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/193.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.193.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/194.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.194.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/195.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.195.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/196.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.196.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/197.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.197.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/198.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.198.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/199.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.199.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/19.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.19.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/1.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.1.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/200.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.200.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/201.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.201.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/202.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.202.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/203.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.203.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/204.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.204.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/205.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.205.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/206.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.206.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/207.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.207.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/208.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.208.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/209.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.209.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/20.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.20.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/210.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.210.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/211.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.211.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/212.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.212.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/213.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.213.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/214.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.214.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/215.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.215.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/216.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.216.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/217.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.217.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/218.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.218.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/219.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.219.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/21.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.21.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/220.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.220.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/221.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.221.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/222.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.222.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/223.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.223.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/224.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.224.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/225.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.225.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/226.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.226.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/227.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.227.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/228.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.228.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/229.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.229.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/22.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.22.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/230.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.230.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/231.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.231.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/232.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.232.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/233.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.233.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/234.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.234.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/235.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.235.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/236.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.236.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/237.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.237.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/238.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.238.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/239.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.239.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/23.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.23.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/240.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.240.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/241.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.241.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/242.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.242.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/243.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.243.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/244.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.244.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/245.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.245.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/246.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.246.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/247.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.247.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/248.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.248.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/249.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.249.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/24.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.24.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/250.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.250.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/251.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.251.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/252.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.252.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/253.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.253.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/254.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.254.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/255.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.255.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/256.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.256.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/257.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.257.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/258.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.258.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/259.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.259.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/25.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.25.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/260.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.260.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/261.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.261.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/262.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.262.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/263.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.263.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/264.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.264.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/265.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.265.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/266.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.266.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/267.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.267.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/268.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.268.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/269.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.269.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/26.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.26.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/270.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.270.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/271.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.271.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/272.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.272.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/273.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.273.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/274.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.274.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/275.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.275.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/276.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.276.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/277.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.277.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/278.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.278.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/279.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.279.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/27.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.27.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/280.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.280.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/281.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.281.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/282.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.282.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/283.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.283.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/284.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.284.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/285.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.285.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/286.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.286.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/287.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.287.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/288.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.288.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/289.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.289.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/28.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.28.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/290.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.290.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/291.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.291.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/292.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.292.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/293.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.293.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/294.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.294.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/295.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.295.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/296.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.296.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/297.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.297.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/298.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.298.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/299.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.299.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/29.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.29.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/2.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.2.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/300.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.300.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/301.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.301.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/302.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.302.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/303.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.303.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/304.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.304.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/305.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.305.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/306.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.306.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/307.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.307.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/308.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.308.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/309.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.309.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/30.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.30.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/310.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.310.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/311.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.311.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/312.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.312.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/313.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.313.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/314.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.314.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/315.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.315.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/316.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.316.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/317.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.317.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/318.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.318.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/319.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.319.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/31.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.31.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/320.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.320.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/321.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.321.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/322.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.322.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/323.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.323.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/324.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.324.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/325.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.325.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/326.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.326.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/327.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.327.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/328.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.328.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/329.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.329.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/32.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.32.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/330.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.330.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/331.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.331.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/332.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.332.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/333.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.333.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/334.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.334.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/335.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.335.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/336.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.336.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/337.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.337.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/338.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.338.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/339.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.339.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/33.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.33.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/340.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.340.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/341.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.341.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/342.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.342.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/343.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.343.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/344.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.344.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/345.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.345.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/346.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.346.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/347.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.347.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/348.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.348.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/349.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.349.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/34.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.34.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/350.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.350.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/351.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.351.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/352.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.352.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/353.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.353.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/354.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.354.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/355.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.355.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/356.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.356.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/357.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.357.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/358.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.358.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/359.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.359.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/35.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.35.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/360.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.360.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/361.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.361.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/362.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.362.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/363.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.363.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/364.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.364.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/365.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.365.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/366.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.366.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/367.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.367.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/368.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.368.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/369.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.369.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/36.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.36.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/370.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.370.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/371.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.371.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/372.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.372.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/373.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.373.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/374.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.374.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/375.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.375.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/376.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.376.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/377.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.377.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/378.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.378.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/379.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.379.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/37.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.37.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/380.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.380.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/381.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.381.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/382.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.382.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/383.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.383.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/384.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.384.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/385.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.385.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/386.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.386.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/387.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.387.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/388.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.388.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/389.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.389.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/38.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.38.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/390.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.390.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/391.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.391.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/392.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.392.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/393.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.393.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/394.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.394.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/395.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.395.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/396.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.396.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/397.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.397.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/398.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.398.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/399.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.399.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/39.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.39.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/3.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.3.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/400.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.400.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/401.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.401.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/402.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.402.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/403.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.403.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/404.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.404.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/405.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.405.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/406.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.406.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/407.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.407.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/408.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.408.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/409.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.409.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/40.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.40.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/410.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.410.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/411.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.411.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/412.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.412.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/413.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.413.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/414.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.414.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/415.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.415.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/416.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.416.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/417.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.417.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/418.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.418.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/419.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.419.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/41.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.41.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/420.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.420.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/421.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.421.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/422.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.422.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/423.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.423.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/424.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.424.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/425.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.425.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/426.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.426.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/427.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.427.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/428.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.428.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/429.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.429.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/42.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.42.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/430.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.430.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/431.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.431.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/432.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.432.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/433.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.433.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/434.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.434.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/435.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.435.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/436.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.436.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/437.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.437.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/438.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.438.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/439.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.439.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/43.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.43.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/440.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.440.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/441.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.441.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/442.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.442.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/443.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.443.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/444.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.444.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/445.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.445.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/446.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.446.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/447.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.447.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/448.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.448.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/449.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.449.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/44.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.44.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/450.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.450.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/451.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.451.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/452.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.452.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/453.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.453.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/454.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.454.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/455.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.455.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/456.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.456.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/457.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.457.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/458.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.458.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/459.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.459.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/45.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.45.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/460.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.460.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/461.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.461.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/462.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.462.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/463.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.463.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/464.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.464.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/465.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.465.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/466.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.466.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/467.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.467.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/468.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.468.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/469.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.469.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/46.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.46.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/470.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.470.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/471.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.471.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/472.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.472.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/473.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.473.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/474.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.474.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/475.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.475.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/476.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.476.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/477.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.477.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/478.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.478.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/479.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.479.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/47.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.47.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/480.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.480.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/481.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.481.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/482.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.482.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/483.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.483.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/484.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.484.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/485.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.485.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/486.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.486.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/487.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.487.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/488.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.488.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/489.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.489.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/48.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.48.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/490.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.490.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/491.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.491.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/492.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.492.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/493.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.493.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/494.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.494.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/495.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.495.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/496.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.496.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/497.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.497.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/498.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.498.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/499.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.499.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/49.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.49.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/4.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.4.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/500.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.500.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/501.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.501.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/502.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.502.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/503.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.503.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/504.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.504.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/505.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.505.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/506.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.506.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/507.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.507.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/508.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.508.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/509.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.509.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/50.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.50.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/510.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.510.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/511.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.511.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/512.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.512.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/513.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.513.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/514.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.514.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/515.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.515.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/516.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.516.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/517.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.517.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/518.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.518.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/519.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.519.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/51.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.51.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/520.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.520.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/521.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.521.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/522.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.522.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/523.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.523.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/524.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.524.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/525.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.525.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/526.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.526.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/527.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.527.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/528.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.528.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/529.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.529.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/52.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.52.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/530.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.530.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/531.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.531.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/532.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.532.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/533.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.533.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/534.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.534.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/535.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.535.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/536.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.536.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/537.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.537.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/538.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.538.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/539.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.539.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/53.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.53.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/540.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.540.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/541.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.541.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/542.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.542.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/543.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.543.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/544.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.544.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/545.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.545.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/546.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.546.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/547.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.547.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/548.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.548.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/549.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.549.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/54.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.54.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/550.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.550.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/551.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.551.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/552.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.552.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/553.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.553.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/554.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.554.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/555.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.555.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/556.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.556.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/557.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.557.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/558.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.558.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/559.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.559.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/55.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.55.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/560.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.560.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/561.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.561.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/562.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.562.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/563.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.563.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/564.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.564.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/565.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.565.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/566.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.566.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/567.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.567.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/568.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.568.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/569.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.569.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/56.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.56.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/570.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.570.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/571.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.571.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/572.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.572.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/573.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.573.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/574.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.574.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/575.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.575.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/576.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.576.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/577.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.577.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/578.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.578.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/579.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.579.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/57.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.57.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/580.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.580.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/581.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.581.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/582.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.582.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/583.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.583.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/584.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.584.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/585.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.585.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/586.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.586.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/587.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.587.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/588.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.588.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/589.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.589.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/58.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.58.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/590.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.590.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/591.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.591.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/592.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.592.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/593.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.593.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/594.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.594.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/595.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.595.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/596.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.596.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/597.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.597.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/598.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.598.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/599.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.599.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/59.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.59.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/5.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.5.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/600.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.600.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/601.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.601.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/602.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.602.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/603.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.603.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/604.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.604.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/605.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.605.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/606.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.606.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/607.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.607.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/608.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.608.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/609.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.609.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/60.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.60.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/610.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.610.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/611.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.611.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/612.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.612.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/613.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.613.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/614.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.614.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/615.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.615.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/616.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.616.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/617.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.617.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/618.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.618.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/619.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.619.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/61.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.61.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/620.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.620.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/621.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.621.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/622.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.622.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/623.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.623.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/624.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.624.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/625.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.625.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/626.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.626.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/627.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.627.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/628.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.628.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/629.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.629.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/62.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.62.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/630.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.630.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/631.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.631.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/632.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.632.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/633.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.633.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/634.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.634.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/635.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.635.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/636.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.636.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/637.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.637.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/638.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.638.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/639.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.639.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/63.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.63.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/640.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.640.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/641.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.641.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/642.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.642.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/643.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.643.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/644.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.644.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/645.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.645.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/64.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.64.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/65.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.65.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/66.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.66.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/67.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.67.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/68.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.68.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/69.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.69.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/6.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.6.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/70.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.70.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/71.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.71.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/72.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.72.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/73.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.73.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/74.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.74.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/75.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.75.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/76.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.76.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/77.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.77.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/78.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.78.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/79.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.79.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/7.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.7.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/80.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.80.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/81.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.81.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/82.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.82.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/83.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.83.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/84.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.84.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/85.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.85.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/86.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.86.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/87.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.87.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/88.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.88.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/89.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.89.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/8.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.8.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/90.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.90.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/91.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.91.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/92.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.92.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/93.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.93.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/94.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.94.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/95.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.95.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/96.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.96.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/97.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.97.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/98.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.98.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/99.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.99.tombo.CG-only -m5C-only -CG-only
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/TomboSingleReadsExtract-tombo_de_novo.py /oak/stanford/groups/wjg/zshipony/Nanopore/Alkylation/2019_04_24_S2_Alkylation/output/tombo_denovo/9.tombo.per_read_stats /oak/stanford/groups/akundaje/marinovg/genomes/dm3/sequence/dm3.fa 2019_04_24_S2_Alkylation.9.tombo.CG-only -m5C-only -CG-only