python ~/code/PEFastqToTabDelimited.py L368-DNAse_no_zymo.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L368-DNAse_no_zymo.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Fungi/Chytridiomycota/Rhizoclosmatium_globosum_JEL800-Rhihy1/bowtie-indexes/GCA_002104985.1_Rhihy1_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Fungi/Chytridiomycota/Rhizoclosmatium_globosum_JEL800-Rhihy1/bowtie-indexes/GCA_002104985.1_Rhihy1_genomic.fa - | ~/programs/samtools-0.1.18/samtools sort - L368-DNAse_no_zymo.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L369-DNAse_DTT_zymo.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L369-DNAse_DTT_zymo.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Fungi/Chytridiomycota/Rhizoclosmatium_globosum_JEL800-Rhihy1/bowtie-indexes/GCA_002104985.1_Rhihy1_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Fungi/Chytridiomycota/Rhizoclosmatium_globosum_JEL800-Rhihy1/bowtie-indexes/GCA_002104985.1_Rhihy1_genomic.fa - | ~/programs/samtools-0.1.18/samtools sort - L369-DNAse_DTT_zymo.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L372-noDNAse_DTT_zymo.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L372-noDNAse_DTT_zymo.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Fungi/Chytridiomycota/Rhizoclosmatium_globosum_JEL800-Rhihy1/bowtie-indexes/GCA_002104985.1_Rhihy1_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Fungi/Chytridiomycota/Rhizoclosmatium_globosum_JEL800-Rhihy1/bowtie-indexes/GCA_002104985.1_Rhihy1_genomic.fa - | ~/programs/samtools-0.1.18/samtools sort - L372-noDNAse_DTT_zymo.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L373-noDNAse_bME_zymo.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L373-noDNAse_bME_zymo.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Fungi/Chytridiomycota/Rhizoclosmatium_globosum_JEL800-Rhihy1/bowtie-indexes/GCA_002104985.1_Rhihy1_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Fungi/Chytridiomycota/Rhizoclosmatium_globosum_JEL800-Rhihy1/bowtie-indexes/GCA_002104985.1_Rhihy1_genomic.fa - | ~/programs/samtools-0.1.18/samtools sort - L373-noDNAse_bME_zymo.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L391-Rosenblatt_Hannah-WT-YPGE.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L391-Rosenblatt_Hannah-WT-YPGE.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L391-Rosenblatt_Hannah-WT-YPGE.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L392-Rosenblatt_Hannah-Asf1-YPD.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L392-Rosenblatt_Hannah-Asf1-YPD.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L392-Rosenblatt_Hannah-Asf1-YPD.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L393-Goddard_Page-Asf1-YPGE.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L393-Goddard_Page-Asf1-YPGE.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L393-Goddard_Page-Asf1-YPGE.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L394-Goddard_Page-Rtt109-YPD.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L394-Goddard_Page-Rtt109-YPD.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L394-Goddard_Page-Rtt109-YPD.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L395-Wong_Wong-Rtt109-YPGE.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L395-Wong_Wong-Rtt109-YPGE.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L395-Wong_Wong-Rtt109-YPGE.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L396-Wong_Wong-WT-YPD.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L396-Wong_Wong-WT-YPD.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L396-Wong_Wong-WT-YPD.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L397-Ngo_Keri-WT-YPGE.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L397-Ngo_Keri-WT-YPGE.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L397-Ngo_Keri-WT-YPGE.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L398-Ngo_Keri-Rtt109-YPD.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L398-Ngo_Keri-Rtt109-YPD.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L398-Ngo_Keri-Rtt109-YPD.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L401-Benjamin_Alyssa-Rtt109-YPGE.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L401-Benjamin_Alyssa-Rtt109-YPGE.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L401-Benjamin_Alyssa-Rtt109-YPGE.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L402-Benjamin_Alyssa-Asf1-YPD.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L402-Benjamin_Alyssa-Asf1-YPD.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L402-Benjamin_Alyssa-Asf1-YPD.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L403-Koska_Mervenaz-WT-YPGE.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L403-Koska_Mervenaz-WT-YPGE.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L403-Koska_Mervenaz-WT-YPGE.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L404-Koska_Mervenaz-Asf1-YPD.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L404-Koska_Mervenaz-Asf1-YPD.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L404-Koska_Mervenaz-Asf1-YPD.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L405-Cotter_Daniel-Asf1-YPGE.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L405-Cotter_Daniel-Asf1-YPGE.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L405-Cotter_Daniel-Asf1-YPGE.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L406-Cotter_Daniel-Rtt109-YPD.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L406-Cotter_Daniel-Rtt109-YPD.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L406-Cotter_Daniel-Rtt109-YPD.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L407-Cheng_Jason-Rtt109-YPGE.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L407-Cheng_Jason-Rtt109-YPGE.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L407-Cheng_Jason-Rtt109-YPGE.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L408-Cheng_Jason-WT-YPD.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L408-Cheng_Jason-WT-YPD.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L408-Cheng_Jason-WT-YPD.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L409-Patel_Roshni-WT-YPGE.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L409-Patel_Roshni-WT-YPGE.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L409-Patel_Roshni-WT-YPGE.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L410-Patel_Roshni-Asf1-YPGE.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L410-Patel_Roshni-Asf1-YPGE.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L410-Patel_Roshni-Asf1-YPGE.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L411-Rutledge_Jarod-Asf1-YPGE.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L411-Rutledge_Jarod-Asf1-YPGE.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L411-Rutledge_Jarod-Asf1-YPGE.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L412-Rutledge_Jarod-Rtt109-YPGE.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L412-Rutledge_Jarod-Rtt109-YPGE.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L412-Rutledge_Jarod-Rtt109-YPGE.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L413-Tomins_Kelly-Rtt109-YPGE.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L413-Tomins_Kelly-Rtt109-YPGE.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L413-Tomins_Kelly-Rtt109-YPGE.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L414-Tomins_Kelly-WT-YPGE.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L414-Tomins_Kelly-WT-YPGE.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L414-Tomins_Kelly-WT-YPGE.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L415-Amador_Gabriel-WT-YPGE.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L415-Amador_Gabriel-WT-YPGE.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L415-Amador_Gabriel-WT-YPGE.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L416-Amador_Gabriel-Rtt109-YPGE.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L416-Amador_Gabriel-Rtt109-YPGE.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L416-Amador_Gabriel-Rtt109-YPGE.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L417-Ungar_Rachel-Asf1-YPGE.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L417-Ungar_Rachel-Asf1-YPGE.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L417-Ungar_Rachel-Asf1-YPGE.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L418-Ungar_Rachel-WT-YPD.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L418-Ungar_Rachel-WT-YPD.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L418-Ungar_Rachel-WT-YPD.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L419-Ma_Rosa-Rtt109-YPD.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L419-Ma_Rosa-Rtt109-YPD.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L419-Ma_Rosa-Rtt109-YPD.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L420-Ma_Rosa-Asf1-YPD.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L420-Ma_Rosa-Asf1-YPD.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L420-Ma_Rosa-Asf1-YPD.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L421-Maghini_Dylan-WT-YPD.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L421-Maghini_Dylan-WT-YPD.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L421-Maghini_Dylan-WT-YPD.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L422-Maghini_Dylan-Asf1-YPD.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L422-Maghini_Dylan-Asf1-YPD.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L422-Maghini_Dylan-Asf1-YPD.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L423-Greenwald_Emily-Asf1-YPD.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L423-Greenwald_Emily-Asf1-YPD.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L423-Greenwald_Emily-Asf1-YPD.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L424-Greenwald_Emily-Rtt109-YPD.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L424-Greenwald_Emily-Rtt109-YPD.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L424-Greenwald_Emily-Rtt109-YPD.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L425-Hanson_Kathryn-Rtt109-YPD.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L425-Hanson_Kathryn-Rtt109-YPD.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L425-Hanson_Kathryn-Rtt109-YPD.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L426-Hanson_Kathryn-WT-YPD.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L426-Hanson_Kathryn-WT-YPD.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L426-Hanson_Kathryn-WT-YPD.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L427-YPD-WT-rep1.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz,~/ENCODE4/datasets-ATAC/L427-YPD-WT-rep1/L427_S1_L001_R1_001.fastq.gz L427-YPD-WT-rep1.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz,~/ENCODE4/datasets-ATAC/L427-YPD-WT-rep1/L427_S1_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L427-YPD-WT-rep1.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L428-YPD-WT-rep2.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz,~/ENCODE4/datasets-ATAC/L428-YPD-WT-rep2/L428_S2_L001_R1_001.fastq.gz L428-YPD-WT-rep2.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz,~/ENCODE4/datasets-ATAC/L428-YPD-WT-rep2/L428_S2_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L428-YPD-WT-rep2.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L429-YPD-asf1-rep1.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz,~/ENCODE4/datasets-ATAC/L429-YPD-asf1-rep1/L429_S3_L001_R1_001.fastq.gz L429-YPD-asf1-rep1.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz,~/ENCODE4/datasets-ATAC/L429-YPD-asf1-rep1/L429_S3_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L429-YPD-asf1-rep1.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L430-YPD-asf1-rep2.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz,~/ENCODE4/datasets-ATAC/L430-YPD-asf1-rep2/L430_S4_L001_R1_001.fastq.gz L430-YPD-asf1-rep2.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz,~/ENCODE4/datasets-ATAC/L430-YPD-asf1-rep2/L430_S4_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L430-YPD-asf1-rep2.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L431-YPD-rtt109-rep1.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz,~/ENCODE4/datasets-ATAC/L431-YPD-rtt109-rep1/L431_S5_L001_R1_001.fastq.gz L431-YPD-rtt109-rep1.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz,~/ENCODE4/datasets-ATAC/L431-YPD-rtt109-rep1/L431_S5_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L431-YPD-rtt109-rep1.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L432-YPD-rtt109-rep2.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz,~/ENCODE4/datasets-ATAC/L432-YPD-rtt109-rep2/L432_S6_L001_R1_001.fastq.gz L432-YPD-rtt109-rep2.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz,~/ENCODE4/datasets-ATAC/L432-YPD-rtt109-rep2/L432_S6_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L432-YPD-rtt109-rep2.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L433-YPGE-WT-rep1.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz,~/ENCODE4/datasets-ATAC/L433-YPGE-WT-rep1/L433_S7_L001_R1_001.fastq.gz L433-YPGE-WT-rep1.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz,~/ENCODE4/datasets-ATAC/L433-YPGE-WT-rep1/L433_S7_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L433-YPGE-WT-rep1.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L434-YPGE-WT-rep2.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz,~/ENCODE4/datasets-ATAC/L434-YPGE-WT-rep2/L434_S8_L001_R1_001.fastq.gz L434-YPGE-WT-rep2.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz,~/ENCODE4/datasets-ATAC/L434-YPGE-WT-rep2/L434_S8_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L434-YPGE-WT-rep2.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L435-YPGE-asf1-rep1.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz,~/ENCODE4/datasets-ATAC/L435-YPGE-asf1-rep1/L435_S9_L001_R1_001.fastq.gz L435-YPGE-asf1-rep1.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz,~/ENCODE4/datasets-ATAC/L435-YPGE-asf1-rep1/L435_S9_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L435-YPGE-asf1-rep1.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L436-YPGE-asf1-rep2.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz,~/ENCODE4/datasets-ATAC/L436-YPGE-asf1-rep2/L436_S10_L001_R1_001.fastq.gz L436-YPGE-asf1-rep2.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz,~/ENCODE4/datasets-ATAC/L436-YPGE-asf1-rep2/L436_S10_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L436-YPGE-asf1-rep2.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L437-YPGE-rtt109-rep1.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz,~/ENCODE4/datasets-ATAC/L437-YPGE-spt10-rep1/L437_S11_L001_R1_001.fastq.gz L437-YPGE-rtt109-rep1.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz,~/ENCODE4/datasets-ATAC/L437-YPGE-spt10-rep1/L437_S11_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L437-YPGE-rtt109-rep1.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L438-YPGE-rtt109-rep2.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz,~/ENCODE4/datasets-ATAC/L438-YPGE-spt10-rep2/L438_S12_L001_R1_001.fastq.gz L438-YPGE-rtt109-rep2.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz,~/ENCODE4/datasets-ATAC/L438-YPGE-spt10-rep2/L438_S12_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L438-YPGE-rtt109-rep2.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L439-YPD-spt10-rep1.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz,~/ENCODE4/datasets-ATAC/L439-YPD-spt10-rep1/L439_S13_L001_R1_001.fastq.gz L439-YPD-spt10-rep1.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz,~/ENCODE4/datasets-ATAC/L439-YPD-spt10-rep1/L439_S13_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L439-YPD-spt10-rep1.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L440-YPD-spt10-rep2.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz,~/ENCODE4/datasets-ATAC/L440-YPD-spt10-rep2/L440_S14_L001_R1_001.fastq.gz L440-YPD-spt10-rep2.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz,~/ENCODE4/datasets-ATAC/L440-YPD-spt10-rep2/L440_S14_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L440-YPD-spt10-rep2.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L441-YPD-rlf2-rep1.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz,~/ENCODE4/datasets-ATAC/L441-YPD-rlf2-rep1/L441_S15_L001_R1_001.fastq.gz L441-YPD-rlf2-rep1.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz,~/ENCODE4/datasets-ATAC/L441-YPD-rlf2-rep1/L441_S15_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L441-YPD-rlf2-rep1.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L442-YPD-rlf2-rep2.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz,~/ENCODE4/datasets-ATAC/L442-YPD-rlf2-rep2/L442_S16_L001_R1_001.fastq.gz L442-YPD-rlf2-rep2.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz,~/ENCODE4/datasets-ATAC/L442-YPD-rlf2-rep2/L442_S16_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L442-YPD-rlf2-rep2.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L443-YPD-hir1-rep1.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz,~/ENCODE4/datasets-ATAC/L443-YPD-hir1-rep1/L443_S17_L001_R1_001.fastq.gz L443-YPD-hir1-rep1.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz,~/ENCODE4/datasets-ATAC/L443-YPD-hir1-rep1/L443_S17_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L443-YPD-hir1-rep1.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L444-YPD-hir1-rep2.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz,~/ENCODE4/datasets-ATAC/L444-YPD-hir1-rep2/L444_S18_L001_R1_001.fastq.gz L444-YPD-hir1-rep2.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz,~/ENCODE4/datasets-ATAC/L444-YPD-hir1-rep2/L444_S18_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L444-YPD-hir1-rep2.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L445-YPD-hir2-rep1.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz,~/ENCODE4/datasets-ATAC/L445-YPD-hir2-rep1/L445_S19_L001_R1_001.fastq.gz L445-YPD-hir2-rep1.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz,~/ENCODE4/datasets-ATAC/L445-YPD-hir2-rep1/L445_S19_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L445-YPD-hir2-rep1.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L446-YPD-hir2-rep2.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz,~/ENCODE4/datasets-ATAC/L446-YPD-hir2-rep2/L446_S20_L001_R1_001.fastq.gz L446-YPD-hir2-rep2.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz,~/ENCODE4/datasets-ATAC/L446-YPD-hir2-rep2/L446_S20_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L446-YPD-hir2-rep2.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L447-YPD-hir3-rep1.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz,~/ENCODE4/datasets-ATAC/L447-YPD-hir3-rep1/L447_S21_L001_R1_001.fastq.gz L447-YPD-hir3-rep1.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz,~/ENCODE4/datasets-ATAC/L447-YPD-hir3-rep1/L447_S21_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L447-YPD-hir3-rep1.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L448-YPD-hir3-rep2.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz,~/ENCODE4/datasets-ATAC/L448-YPD-hir3-rep2/L448_S22_L001_R1_001.fastq.gz L448-YPD-hir3-rep2.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz,~/ENCODE4/datasets-ATAC/L448-YPD-hir3-rep2/L448_S22_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L448-YPD-hir3-rep2.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L449-YPD-hpc2-rep1.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz,~/ENCODE4/datasets-ATAC/L449-YPD-hpc2-rep1/L449_S23_L001_R1_001.fastq.gz L449-YPD-hpc2-rep1.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz,~/ENCODE4/datasets-ATAC/L449-YPD-hpc2-rep1/L449_S23_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L449-YPD-hpc2-rep1.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L450-YPD-hpc2-rep2.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz,~/ENCODE4/datasets-ATAC/L450-YPD-hpc2-rep2/L450_S24_L001_R1_001.fastq.gz L450-YPD-hpc2-rep2.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz,~/ENCODE4/datasets-ATAC/L450-YPD-hpc2-rep2/L450_S24_L001_R2_001.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/sacCer3/bowtie-indexes/sacCer3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/sacCer3/bowtie-indexes/sacCer3.fa - | ~/programs/samtools-0.1.18/samtools sort - L450-YPD-hpc2-rep2.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L451-1x_cells.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L451-1x_cells.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Fungi/Chytridiomycota/Rhizoclosmatium_globosum_JEL800-Rhihy1/bowtie-indexes/GCA_002104985.1_Rhihy1_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Fungi/Chytridiomycota/Rhizoclosmatium_globosum_JEL800-Rhihy1/bowtie-indexes/GCA_002104985.1_Rhihy1_genomic.fa - | ~/programs/samtools-0.1.18/samtools sort - L451-1x_cells.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L452-1x_cells_RSB.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L452-1x_cells_RSB.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Fungi/Chytridiomycota/Rhizoclosmatium_globosum_JEL800-Rhihy1/bowtie-indexes/GCA_002104985.1_Rhihy1_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Fungi/Chytridiomycota/Rhizoclosmatium_globosum_JEL800-Rhihy1/bowtie-indexes/GCA_002104985.1_Rhihy1_genomic.fa - | ~/programs/samtools-0.1.18/samtools sort - L452-1x_cells_RSB.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L453-4x_cells.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L453-4x_cells.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Fungi/Chytridiomycota/Rhizoclosmatium_globosum_JEL800-Rhihy1/bowtie-indexes/GCA_002104985.1_Rhihy1_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Fungi/Chytridiomycota/Rhizoclosmatium_globosum_JEL800-Rhihy1/bowtie-indexes/GCA_002104985.1_Rhihy1_genomic.fa - | ~/programs/samtools-0.1.18/samtools sort - L453-4x_cells.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L459-GM18278_3_minutes_ATAC.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L459-GM18278_3_minutes_ATAC.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg19/bowtie-indexes/hg19-female -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/hg19/bowtie-indexes/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - L459-GM18278_3_minutes_ATAC.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L460-GM18278_5_minutes_ATAC.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L460-GM18278_5_minutes_ATAC.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg19/bowtie-indexes/hg19-female -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/hg19/bowtie-indexes/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - L460-GM18278_5_minutes_ATAC.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L461-GM18278_10_minutes_ATAC.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L461-GM18278_10_minutes_ATAC.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg19/bowtie-indexes/hg19-female -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/hg19/bowtie-indexes/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - L461-GM18278_10_minutes_ATAC.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L462-GM18278_15_minutes_ATAC.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L462-GM18278_15_minutes_ATAC.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg19/bowtie-indexes/hg19-female -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/hg19/bowtie-indexes/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - L462-GM18278_15_minutes_ATAC.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L463-GM18278_30_minutes_ATAC.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L463-GM18278_30_minutes_ATAC.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg19/bowtie-indexes/hg19-female -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/hg19/bowtie-indexes/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - L463-GM18278_30_minutes_ATAC.2x36mers.unique
python ~/code/PEFastqToTabDelimited.py L459-GM18278_3_minutes_ATAC.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L459-GM18278_3_minutes_ATAC.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg19/bowtie-indexes/hg19-chrM -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/hg19/bowtie-indexes/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - L459-GM18278_3_minutes_ATAC.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py L460-GM18278_5_minutes_ATAC.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L460-GM18278_5_minutes_ATAC.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg19/bowtie-indexes/hg19-chrM -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/hg19/bowtie-indexes/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - L460-GM18278_5_minutes_ATAC.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py L461-GM18278_10_minutes_ATAC.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L461-GM18278_10_minutes_ATAC.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg19/bowtie-indexes/hg19-chrM -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/hg19/bowtie-indexes/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - L461-GM18278_10_minutes_ATAC.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py L462-GM18278_15_minutes_ATAC.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L462-GM18278_15_minutes_ATAC.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg19/bowtie-indexes/hg19-chrM -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/hg19/bowtie-indexes/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - L462-GM18278_15_minutes_ATAC.2x36mers.chrM
python ~/code/PEFastqToTabDelimited.py L463-GM18278_30_minutes_ATAC.180909_NB551514_0023_AH5VFFBGX9.end1.fastq.gz L463-GM18278_30_minutes_ATAC.180909_NB551514_0023_AH5VFFBGX9.end2.fastq.gz -trim 36 36 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg19/bowtie-indexes/hg19-chrM -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/hg19/bowtie-indexes/hg19.fa - | ~/programs/samtools-0.1.18/samtools sort - L463-GM18278_30_minutes_ATAC.2x36mers.chrM