zcat Homo_sapiens-non-identifiable_human_individual-liver-H3K4me3-ERR572159.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg20/bowtie-indexes/hg38-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/hg20/sequence/hg38.fa - | ~/programs/samtools-0.1.18/samtools sort - Homo_sapiens-non-identifiable_human_individual-liver-H3K4me3-ERR572159.50mers.unique
zcat Homo_sapiens-non-identifiable_human_individual-liver-H3K4me3-ERR572248.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg20/bowtie-indexes/hg38-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/hg20/sequence/hg38.fa - | ~/programs/samtools-0.1.18/samtools sort - Homo_sapiens-non-identifiable_human_individual-liver-H3K4me3-ERR572248.50mers.unique
zcat Homo_sapiens-non-identifiable_human_individual-liver-H3K4me3-ERR572284.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg20/bowtie-indexes/hg38-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/hg20/sequence/hg38.fa - | ~/programs/samtools-0.1.18/samtools sort - Homo_sapiens-non-identifiable_human_individual-liver-H3K4me3-ERR572284.50mers.unique
zcat Homo_sapiens-non-identifiable_human_individual-liver-H3K4me3-ERR572270.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg20/bowtie-indexes/hg38-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/hg20/sequence/hg38.fa - | ~/programs/samtools-0.1.18/samtools sort - Homo_sapiens-non-identifiable_human_individual-liver-H3K4me3-ERR572270.50mers.unique
zcat Homo_sapiens-non-identifiable_human_individual-liver-H3K27Ac_-ERR572148.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg20/bowtie-indexes/hg38-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/hg20/sequence/hg38.fa - | ~/programs/samtools-0.1.18/samtools sort - Homo_sapiens-non-identifiable_human_individual-liver-H3K27Ac-ERR572148.50mers.unique
zcat Homo_sapiens-non-identifiable_human_individual-liver-H3K27Ac_-ERR572241.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg20/bowtie-indexes/hg38-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/hg20/sequence/hg38.fa - | ~/programs/samtools-0.1.18/samtools sort - Homo_sapiens-non-identifiable_human_individual-liver-H3K27Ac-ERR572241.50mers.unique
zcat Homo_sapiens-non-identifiable_human_individual-liver-H3K27Ac_-ERR572285.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg20/bowtie-indexes/hg38-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/hg20/sequence/hg38.fa - | ~/programs/samtools-0.1.18/samtools sort - Homo_sapiens-non-identifiable_human_individual-liver-H3K27Ac-ERR572285.50mers.unique
zcat Homo_sapiens-non-identifiable_human_individual-liver-H3K27Ac_-ERR572151.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg20/bowtie-indexes/hg38-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/hg20/sequence/hg38.fa - | ~/programs/samtools-0.1.18/samtools sort - Homo_sapiens-non-identifiable_human_individual-liver-H3K27Ac-ERR572151.50mers.unique
zcat Homo_sapiens-non-identifiable_human_individual-liver-input-ERR572219.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg20/bowtie-indexes/hg38-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/hg20/sequence/hg38.fa - | ~/programs/samtools-0.1.18/samtools sort - Homo_sapiens-non-identifiable_human_individual-liver-input-ERR572219.50mers.unique
zcat Homo_sapiens-non-identifiable_human_individual-liver-input-ERR572295.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg20/bowtie-indexes/hg38-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/hg20/sequence/hg38.fa - | ~/programs/samtools-0.1.18/samtools sort - Homo_sapiens-non-identifiable_human_individual-liver-input-ERR572295.50mers.unique
zcat Homo_sapiens-non-identifiable_human_individual-liver-input-ERR572249.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg20/bowtie-indexes/hg38-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/hg20/sequence/hg38.fa - | ~/programs/samtools-0.1.18/samtools sort - Homo_sapiens-non-identifiable_human_individual-liver-input-ERR572249.50mers.unique
zcat Homo_sapiens-non-identifiable_human_individual-liver-input-ERR572195.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/hg20/bowtie-indexes/hg38-male -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/hg20/sequence/hg38.fa - | ~/programs/samtools-0.1.18/samtools sort - Homo_sapiens-non-identifiable_human_individual-liver-input-ERR572195.50mers.unique
zcat Macaca_mulatta-male-liver-H3K4me3-ERR572234.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Macaca_mulatta.MMUL_1/bowtie-indexes/Macaca_mulatta.MMUL_1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Macaca_mulatta.MMUL_1/bowtie-indexes/Macaca_mulatta.MMUL_1.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Macaca_mulatta-male-liver-H3K4me3-ERR572234.50mers.unique
zcat Macaca_mulatta-male-liver-H3K4me3-ERR572245.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Macaca_mulatta.MMUL_1/bowtie-indexes/Macaca_mulatta.MMUL_1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Macaca_mulatta.MMUL_1/bowtie-indexes/Macaca_mulatta.MMUL_1.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Macaca_mulatta-male-liver-H3K4me3-ERR572245.50mers.unique
zcat Macaca_mulatta-male-liver-H3K4me3-ERR572239.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Macaca_mulatta.MMUL_1/bowtie-indexes/Macaca_mulatta.MMUL_1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Macaca_mulatta.MMUL_1/bowtie-indexes/Macaca_mulatta.MMUL_1.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Macaca_mulatta-male-liver-H3K4me3-ERR572239.50mers.unique
zcat Macaca_mulatta-female-liver-H3K4me3-ERR572255.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Macaca_mulatta.MMUL_1/bowtie-indexes/Macaca_mulatta.MMUL_1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Macaca_mulatta.MMUL_1/bowtie-indexes/Macaca_mulatta.MMUL_1.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Macaca_mulatta-female-liver-H3K4me3-ERR572255.50mers.unique
zcat Macaca_mulatta-male-liver-H3K27Ac-ERR572211.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Macaca_mulatta.MMUL_1/bowtie-indexes/Macaca_mulatta.MMUL_1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Macaca_mulatta.MMUL_1/bowtie-indexes/Macaca_mulatta.MMUL_1.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Macaca_mulatta-male-liver-H3K27Ac-ERR572211.50mers.unique
zcat Macaca_mulatta-male-liver-H3K27Ac-ERR572150.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Macaca_mulatta.MMUL_1/bowtie-indexes/Macaca_mulatta.MMUL_1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Macaca_mulatta.MMUL_1/bowtie-indexes/Macaca_mulatta.MMUL_1.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Macaca_mulatta-male-liver-H3K27Ac-ERR572150.50mers.unique
zcat Macaca_mulatta-male-liver-H3K27Ac-ERR572290.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Macaca_mulatta.MMUL_1/bowtie-indexes/Macaca_mulatta.MMUL_1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Macaca_mulatta.MMUL_1/bowtie-indexes/Macaca_mulatta.MMUL_1.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Macaca_mulatta-male-liver-H3K27Ac-ERR572290.50mers.unique
zcat Macaca_mulatta-female-liver-H3K27Ac-ERR572155.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Macaca_mulatta.MMUL_1/bowtie-indexes/Macaca_mulatta.MMUL_1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Macaca_mulatta.MMUL_1/bowtie-indexes/Macaca_mulatta.MMUL_1.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Macaca_mulatta-female-liver-H3K27Ac-ERR572155.50mers.unique
zcat Macaca_mulatta-male-liver-input-ERR572142.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Macaca_mulatta.MMUL_1/bowtie-indexes/Macaca_mulatta.MMUL_1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Macaca_mulatta.MMUL_1/bowtie-indexes/Macaca_mulatta.MMUL_1.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Macaca_mulatta-male-liver-input-ERR572142.50mers.unique
zcat Macaca_mulatta-male-liver-input-ERR572246.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Macaca_mulatta.MMUL_1/bowtie-indexes/Macaca_mulatta.MMUL_1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Macaca_mulatta.MMUL_1/bowtie-indexes/Macaca_mulatta.MMUL_1.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Macaca_mulatta-male-liver-input-ERR572246.50mers.unique
zcat Macaca_mulatta-male-liver-input-ERR572273.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Macaca_mulatta.MMUL_1/bowtie-indexes/Macaca_mulatta.MMUL_1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Macaca_mulatta.MMUL_1/bowtie-indexes/Macaca_mulatta.MMUL_1.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Macaca_mulatta-male-liver-input-ERR572273.50mers.unique
zcat Macaca_mulatta-female-liver-input-ERR572242.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Macaca_mulatta.MMUL_1/bowtie-indexes/Macaca_mulatta.MMUL_1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Macaca_mulatta.MMUL_1/bowtie-indexes/Macaca_mulatta.MMUL_1.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Macaca_mulatta-female-liver-input-ERR572242.50mers.unique
zcat Chlorocebus_aethiops_sabaeus-female-liver-H3K4me3-ERR572265.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Chlorocebus_aethiops_sabaeus-female-liver-H3K4me3-ERR572265.50mers.unique
zcat Chlorocebus_aethiops_sabaeus-female-liver-H3K4me3-ERR572230.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Chlorocebus_aethiops_sabaeus-female-liver-H3K4me3-ERR572230.50mers.unique
zcat Chlorocebus_aethiops_sabaeus-female-liver-H3K4me3-ERR572183.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Chlorocebus_aethiops_sabaeus-female-liver-H3K4me3-ERR572183.50mers.unique
zcat Chlorocebus_aethiops_sabaeus-female-liver-H3K27Ac-ERR572221.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Chlorocebus_aethiops_sabaeus-female-liver-H3K27Ac-ERR572221.50mers.unique
zcat Chlorocebus_aethiops_sabaeus-female-liver-H3K27Ac-ERR572188.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Chlorocebus_aethiops_sabaeus-female-liver-H3K27Ac-ERR572188.50mers.unique
zcat Chlorocebus_aethiops_sabaeus-female-liver-H3K27Ac-ERR572220.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Chlorocebus_aethiops_sabaeus-female-liver-H3K27Ac-ERR572220.50mers.unique
zcat Chlorocebus_aethiops_sabaeus-female-liver-input-ERR572175.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Chlorocebus_aethiops_sabaeus-female-liver-input-ERR572175.50mers.unique
zcat Chlorocebus_aethiops_sabaeus-female-liver-input-ERR572154.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Chlorocebus_aethiops_sabaeus-female-liver-input-ERR572154.50mers.unique
zcat Chlorocebus_aethiops_sabaeus-female-liver-input-ERR572206.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Chlorocebus_aethiops_sabaeus-female-liver-input-ERR572206.50mers.unique
zcat Callithrix_jacchus-male-liver-H3K4me3-ERR572279.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Callithrix_jacchus.C_jacchus3.2.1/bowtie-indexes/Callithrix_jacchus.C_jacchus3.2.1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Callithrix_jacchus.C_jacchus3.2.1/bowtie-indexes/Callithrix_jacchus.C_jacchus3.2.1.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Callithrix_jacchus-male-liver-H3K4me3-ERR572279.50mers.unique
zcat Callithrix_jacchus-male-liver-H3K4me3-ERR572280.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Callithrix_jacchus.C_jacchus3.2.1/bowtie-indexes/Callithrix_jacchus.C_jacchus3.2.1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Callithrix_jacchus.C_jacchus3.2.1/bowtie-indexes/Callithrix_jacchus.C_jacchus3.2.1.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Callithrix_jacchus-male-liver-H3K4me3-ERR572280.50mers.unique
zcat Callithrix_jacchus-male-liver-H3K4me3-ERR572225.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Callithrix_jacchus.C_jacchus3.2.1/bowtie-indexes/Callithrix_jacchus.C_jacchus3.2.1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Callithrix_jacchus.C_jacchus3.2.1/bowtie-indexes/Callithrix_jacchus.C_jacchus3.2.1.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Callithrix_jacchus-male-liver-H3K4me3-ERR572225.50mers.unique
zcat Callithrix_jacchus-male-liver-H3K27Ac-ERR572209.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Callithrix_jacchus.C_jacchus3.2.1/bowtie-indexes/Callithrix_jacchus.C_jacchus3.2.1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Callithrix_jacchus.C_jacchus3.2.1/bowtie-indexes/Callithrix_jacchus.C_jacchus3.2.1.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Callithrix_jacchus-male-liver-H3K27Ac-ERR572209.50mers.unique
zcat Callithrix_jacchus-male-liver-H3K27Ac-ERR572184.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Callithrix_jacchus.C_jacchus3.2.1/bowtie-indexes/Callithrix_jacchus.C_jacchus3.2.1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Callithrix_jacchus.C_jacchus3.2.1/bowtie-indexes/Callithrix_jacchus.C_jacchus3.2.1.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Callithrix_jacchus-male-liver-H3K27Ac-ERR572184.50mers.unique
zcat Callithrix_jacchus-male-liver-H3K27Ac-ERR572202.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Callithrix_jacchus.C_jacchus3.2.1/bowtie-indexes/Callithrix_jacchus.C_jacchus3.2.1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Callithrix_jacchus.C_jacchus3.2.1/bowtie-indexes/Callithrix_jacchus.C_jacchus3.2.1.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Callithrix_jacchus-male-liver-H3K27Ac-ERR572202.50mers.unique
zcat Callithrix_jacchus-male-liver-input-ERR572189.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Callithrix_jacchus.C_jacchus3.2.1/bowtie-indexes/Callithrix_jacchus.C_jacchus3.2.1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Callithrix_jacchus.C_jacchus3.2.1/bowtie-indexes/Callithrix_jacchus.C_jacchus3.2.1.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Callithrix_jacchus-male-liver-input-ERR572189.50mers.unique
zcat Callithrix_jacchus-male-liver-input-ERR572223.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Callithrix_jacchus.C_jacchus3.2.1/bowtie-indexes/Callithrix_jacchus.C_jacchus3.2.1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Callithrix_jacchus.C_jacchus3.2.1/bowtie-indexes/Callithrix_jacchus.C_jacchus3.2.1.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Callithrix_jacchus-male-liver-input-ERR572223.50mers.unique
zcat Callithrix_jacchus-male-liver-input-ERR572287.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Callithrix_jacchus.C_jacchus3.2.1/bowtie-indexes/Callithrix_jacchus.C_jacchus3.2.1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Callithrix_jacchus.C_jacchus3.2.1/bowtie-indexes/Callithrix_jacchus.C_jacchus3.2.1.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Callithrix_jacchus-male-liver-input-ERR572287.50mers.unique
zcat Mus_musculus_domesticus-male-liver-H3K4me3-ERR572162.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/mm10/bowtie-indexes/mm10 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/mm10/sequence/mm10.fa - | ~/programs/samtools-0.1.18/samtools sort - Mus_musculus_domesticus-male-liver-H3K4me3-ERR572162.50mers.unique
zcat Mus_musculus_domesticus-male-liver-H3K4me3-ERR572240.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/mm10/bowtie-indexes/mm10 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/mm10/sequence/mm10.fa - | ~/programs/samtools-0.1.18/samtools sort - Mus_musculus_domesticus-male-liver-H3K4me3-ERR572240.50mers.unique
zcat Mus_musculus_domesticus-male-liver-H3K4me3-ERR572250.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/mm10/bowtie-indexes/mm10 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/mm10/sequence/mm10.fa - | ~/programs/samtools-0.1.18/samtools sort - Mus_musculus_domesticus-male-liver-H3K4me3-ERR572250.50mers.unique
zcat Mus_musculus_domesticus-male-liver-H3K4me3-ERR572176.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/mm10/bowtie-indexes/mm10 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/mm10/sequence/mm10.fa - | ~/programs/samtools-0.1.18/samtools sort - Mus_musculus_domesticus-male-liver-H3K4me3-ERR572176.50mers.unique
zcat Mus_musculus_domesticus-male-liver-H3K27Ac-ERR572228.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/mm10/bowtie-indexes/mm10 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/mm10/sequence/mm10.fa - | ~/programs/samtools-0.1.18/samtools sort - Mus_musculus_domesticus-male-liver-H3K27Ac-ERR572228.50mers.unique
zcat Mus_musculus_domesticus-male-liver-H3K27Ac-ERR572192.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/mm10/bowtie-indexes/mm10 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/mm10/sequence/mm10.fa - | ~/programs/samtools-0.1.18/samtools sort - Mus_musculus_domesticus-male-liver-H3K27Ac-ERR572192.50mers.unique
zcat Mus_musculus_domesticus-male-liver-H3K27Ac-ERR572141.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/mm10/bowtie-indexes/mm10 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/mm10/sequence/mm10.fa - | ~/programs/samtools-0.1.18/samtools sort - Mus_musculus_domesticus-male-liver-H3K27Ac-ERR572141.50mers.unique
zcat Mus_musculus_domesticus-male-liver-H3K27Ac-ERR572185.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/mm10/bowtie-indexes/mm10 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/mm10/sequence/mm10.fa - | ~/programs/samtools-0.1.18/samtools sort - Mus_musculus_domesticus-male-liver-H3K27Ac-ERR572185.50mers.unique
zcat Mus_musculus_domesticus-male-liver-input-ERR572173.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/mm10/bowtie-indexes/mm10 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/mm10/sequence/mm10.fa - | ~/programs/samtools-0.1.18/samtools sort - Mus_musculus_domesticus-male-liver-input-ERR572173.50mers.unique
zcat Mus_musculus_domesticus-male-liver-input-ERR572140.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/mm10/bowtie-indexes/mm10 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/mm10/sequence/mm10.fa - | ~/programs/samtools-0.1.18/samtools sort - Mus_musculus_domesticus-male-liver-input-ERR572140.50mers.unique
zcat Mus_musculus_domesticus-male-liver-input-ERR572227.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/mm10/bowtie-indexes/mm10 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/mm10/sequence/mm10.fa - | ~/programs/samtools-0.1.18/samtools sort - Mus_musculus_domesticus-male-liver-input-ERR572227.50mers.unique
zcat Mus_musculus_domesticus-male-liver-input-ERR572226.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/mm10/bowtie-indexes/mm10 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/mm10/sequence/mm10.fa - | ~/programs/samtools-0.1.18/samtools sort - Mus_musculus_domesticus-male-liver-input-ERR572226.50mers.unique
zcat Rattus_norvegicus-male-liver-H3K4me3-ERR572172.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/rn6/bowtie-indexes/rn6 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/rn6/sequence/rn6.fa - | ~/programs/samtools-0.1.18/samtools sort - Rattus_norvegicus-male-liver-H3K4me3-ERR572172.50mers.unique
zcat Rattus_norvegicus-male-liver-H3K4me3-ERR572264.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/rn6/bowtie-indexes/rn6 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/rn6/sequence/rn6.fa - | ~/programs/samtools-0.1.18/samtools sort - Rattus_norvegicus-male-liver-H3K4me3-ERR572264.50mers.unique
zcat Rattus_norvegicus-male-liver-H3K4me3-ERR572272.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/rn6/bowtie-indexes/rn6 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/rn6/sequence/rn6.fa - | ~/programs/samtools-0.1.18/samtools sort - Rattus_norvegicus-male-liver-H3K4me3-ERR572272.50mers.unique
zcat Rattus_norvegicus-male-liver-H3K27Ac-ERR572251.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/rn6/bowtie-indexes/rn6 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/rn6/sequence/rn6.fa - | ~/programs/samtools-0.1.18/samtools sort - Rattus_norvegicus-male-liver-H3K27Ac-ERR572251.50mers.unique
zcat Rattus_norvegicus-male-liver-H3K27Ac-ERR572179.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/rn6/bowtie-indexes/rn6 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/rn6/sequence/rn6.fa - | ~/programs/samtools-0.1.18/samtools sort - Rattus_norvegicus-male-liver-H3K27Ac-ERR572179.50mers.unique
zcat Rattus_norvegicus-male-liver-H3K27Ac-ERR572186.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/rn6/bowtie-indexes/rn6 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/rn6/sequence/rn6.fa - | ~/programs/samtools-0.1.18/samtools sort - Rattus_norvegicus-male-liver-H3K27Ac-ERR572186.50mers.unique
zcat Rattus_norvegicus-male-liver-input-ERR572166.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/rn6/bowtie-indexes/rn6 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/rn6/sequence/rn6.fa - | ~/programs/samtools-0.1.18/samtools sort - Rattus_norvegicus-male-liver-input-ERR572166.50mers.unique
zcat Rattus_norvegicus-male-liver-input-ERR572144.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/rn6/bowtie-indexes/rn6 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/rn6/sequence/rn6.fa - | ~/programs/samtools-0.1.18/samtools sort - Rattus_norvegicus-male-liver-input-ERR572144.50mers.unique
zcat Rattus_norvegicus-male-liver-input-ERR572177.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/rn6/bowtie-indexes/rn6 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/rn6/sequence/rn6.fa - | ~/programs/samtools-0.1.18/samtools sort - Rattus_norvegicus-male-liver-input-ERR572177.50mers.unique
zcat Cavia_porcellus-male-liver-H3K4me3-ERR572170.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Cavia_porcellus.cavPor3/bowtie-indexes/Cavia_porcellus.cavPor3.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Cavia_porcellus.cavPor3/bowtie-indexes/Cavia_porcellus.cavPor3.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Cavia_porcellus-male-liver-H3K4me3-ERR572170.50mers.unique
zcat Cavia_porcellus-male-liver-H3K4me3-ERR572201.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Cavia_porcellus.cavPor3/bowtie-indexes/Cavia_porcellus.cavPor3.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Cavia_porcellus.cavPor3/bowtie-indexes/Cavia_porcellus.cavPor3.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Cavia_porcellus-male-liver-H3K4me3-ERR572201.50mers.unique
zcat Cavia_porcellus-male-liver-H3K4me3-ERR572229.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Cavia_porcellus.cavPor3/bowtie-indexes/Cavia_porcellus.cavPor3.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Cavia_porcellus.cavPor3/bowtie-indexes/Cavia_porcellus.cavPor3.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Cavia_porcellus-male-liver-H3K4me3-ERR572229.50mers.unique
zcat Cavia_porcellus-male-liver-H3K27Ac-ERR572149.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Cavia_porcellus.cavPor3/bowtie-indexes/Cavia_porcellus.cavPor3.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Cavia_porcellus.cavPor3/bowtie-indexes/Cavia_porcellus.cavPor3.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Cavia_porcellus-male-liver-H3K27Ac-ERR572149.50mers.unique
zcat Cavia_porcellus-male-liver-H3K27Ac-ERR572281.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Cavia_porcellus.cavPor3/bowtie-indexes/Cavia_porcellus.cavPor3.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Cavia_porcellus.cavPor3/bowtie-indexes/Cavia_porcellus.cavPor3.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Cavia_porcellus-male-liver-H3K27Ac-ERR572281.50mers.unique
zcat Cavia_porcellus-male-liver-H3K27Ac-ERR572182.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Cavia_porcellus.cavPor3/bowtie-indexes/Cavia_porcellus.cavPor3.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Cavia_porcellus.cavPor3/bowtie-indexes/Cavia_porcellus.cavPor3.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Cavia_porcellus-male-liver-H3K27Ac-ERR572182.50mers.unique
zcat Cavia_porcellus-male-liver-input-ERR572215.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Cavia_porcellus.cavPor3/bowtie-indexes/Cavia_porcellus.cavPor3.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Cavia_porcellus.cavPor3/bowtie-indexes/Cavia_porcellus.cavPor3.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Cavia_porcellus-male-liver-input-ERR572215.50mers.unique
zcat Cavia_porcellus-male-liver-input-ERR572146.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Cavia_porcellus.cavPor3/bowtie-indexes/Cavia_porcellus.cavPor3.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Cavia_porcellus.cavPor3/bowtie-indexes/Cavia_porcellus.cavPor3.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Cavia_porcellus-male-liver-input-ERR572146.50mers.unique
zcat Cavia_porcellus-male-liver-input-ERR572269.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Cavia_porcellus.cavPor3/bowtie-indexes/Cavia_porcellus.cavPor3.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Cavia_porcellus.cavPor3/bowtie-indexes/Cavia_porcellus.cavPor3.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Cavia_porcellus-male-liver-input-ERR572269.50mers.unique
zcat Heterocephalus_glaber-male-liver-H3K4me3-ERR572203.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Heterocephalus_glaber-HetGla_female_1.0_hetGal2/bowtie-indexes/GCA_000247695.1_HetGla_female_1.0_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Heterocephalus_glaber-HetGla_female_1.0_hetGal2/bowtie-indexes/GCA_000247695.1_HetGla_female_1.0_genomic.fa - | ~/programs/samtools-0.1.18/samtools sort - Heterocephalus_glaber-male-liver-H3K4me3-ERR572203.50mers.unique
zcat Heterocephalus_glaber-male-liver-H3K4me3-ERR572127.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Heterocephalus_glaber-HetGla_female_1.0_hetGal2/bowtie-indexes/GCA_000247695.1_HetGla_female_1.0_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Heterocephalus_glaber-HetGla_female_1.0_hetGal2/bowtie-indexes/GCA_000247695.1_HetGla_female_1.0_genomic.fa - | ~/programs/samtools-0.1.18/samtools sort - Heterocephalus_glaber-male-liver-H3K4me3-ERR572127.50mers.unique
zcat Heterocephalus_glaber-male-liver-H3K4me3-ERR572276.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Heterocephalus_glaber-HetGla_female_1.0_hetGal2/bowtie-indexes/GCA_000247695.1_HetGla_female_1.0_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Heterocephalus_glaber-HetGla_female_1.0_hetGal2/bowtie-indexes/GCA_000247695.1_HetGla_female_1.0_genomic.fa - | ~/programs/samtools-0.1.18/samtools sort - Heterocephalus_glaber-male-liver-H3K4me3-ERR572276.50mers.unique
zcat Heterocephalus_glaber-male-liver-H3K27Ac-ERR572262.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Heterocephalus_glaber-HetGla_female_1.0_hetGal2/bowtie-indexes/GCA_000247695.1_HetGla_female_1.0_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Heterocephalus_glaber-HetGla_female_1.0_hetGal2/bowtie-indexes/GCA_000247695.1_HetGla_female_1.0_genomic.fa - | ~/programs/samtools-0.1.18/samtools sort - Heterocephalus_glaber-male-liver-H3K27Ac-ERR572262.50mers.unique
zcat Heterocephalus_glaber-male-liver-H3K27Ac-ERR572247.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Heterocephalus_glaber-HetGla_female_1.0_hetGal2/bowtie-indexes/GCA_000247695.1_HetGla_female_1.0_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Heterocephalus_glaber-HetGla_female_1.0_hetGal2/bowtie-indexes/GCA_000247695.1_HetGla_female_1.0_genomic.fa - | ~/programs/samtools-0.1.18/samtools sort - Heterocephalus_glaber-male-liver-H3K27Ac-ERR572247.50mers.unique
zcat Heterocephalus_glaber-male-liver-H3K27Ac-ERR572263.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Heterocephalus_glaber-HetGla_female_1.0_hetGal2/bowtie-indexes/GCA_000247695.1_HetGla_female_1.0_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Heterocephalus_glaber-HetGla_female_1.0_hetGal2/bowtie-indexes/GCA_000247695.1_HetGla_female_1.0_genomic.fa - | ~/programs/samtools-0.1.18/samtools sort - Heterocephalus_glaber-male-liver-H3K27Ac-ERR572263.50mers.unique
zcat Heterocephalus_glaber-male-liver-input-ERR572168.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Heterocephalus_glaber-HetGla_female_1.0_hetGal2/bowtie-indexes/GCA_000247695.1_HetGla_female_1.0_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Heterocephalus_glaber-HetGla_female_1.0_hetGal2/bowtie-indexes/GCA_000247695.1_HetGla_female_1.0_genomic.fa - | ~/programs/samtools-0.1.18/samtools sort - Heterocephalus_glaber-male-liver-input-ERR572168.50mers.unique
zcat Heterocephalus_glaber-male-liver-input-ERR572291.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Heterocephalus_glaber-HetGla_female_1.0_hetGal2/bowtie-indexes/GCA_000247695.1_HetGla_female_1.0_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Heterocephalus_glaber-HetGla_female_1.0_hetGal2/bowtie-indexes/GCA_000247695.1_HetGla_female_1.0_genomic.fa - | ~/programs/samtools-0.1.18/samtools sort - Heterocephalus_glaber-male-liver-input-ERR572291.50mers.unique
zcat Heterocephalus_glaber-male-liver-input-ERR572187.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Heterocephalus_glaber-HetGla_female_1.0_hetGal2/bowtie-indexes/GCA_000247695.1_HetGla_female_1.0_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Heterocephalus_glaber-HetGla_female_1.0_hetGal2/bowtie-indexes/GCA_000247695.1_HetGla_female_1.0_genomic.fa - | ~/programs/samtools-0.1.18/samtools sort - Heterocephalus_glaber-male-liver-input-ERR572187.50mers.unique
zcat Oryctolagus_cuniculus-male-liver-H3K4me3-ERR572213.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Oryctolagus_cuniculus.OryCun2.0/bowtie-indexes/Oryctolagus_cuniculus.OryCun2.0.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Oryctolagus_cuniculus.OryCun2.0/bowtie-indexes/Oryctolagus_cuniculus.OryCun2.0.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Oryctolagus_cuniculus-male-liver-H3K4me3-ERR572213.50mers.unique
zcat Oryctolagus_cuniculus-male-liver-H3K4me3-ERR572153.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Oryctolagus_cuniculus.OryCun2.0/bowtie-indexes/Oryctolagus_cuniculus.OryCun2.0.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Oryctolagus_cuniculus.OryCun2.0/bowtie-indexes/Oryctolagus_cuniculus.OryCun2.0.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Oryctolagus_cuniculus-male-liver-H3K4me3-ERR572153.50mers.unique
zcat Oryctolagus_cuniculus-male-liver-H3K4me3-ERR572267.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Oryctolagus_cuniculus.OryCun2.0/bowtie-indexes/Oryctolagus_cuniculus.OryCun2.0.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Oryctolagus_cuniculus.OryCun2.0/bowtie-indexes/Oryctolagus_cuniculus.OryCun2.0.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Oryctolagus_cuniculus-male-liver-H3K4me3-ERR572267.50mers.unique
zcat Oryctolagus_cuniculus-male-liver-H3K27Ac-ERR572126.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Oryctolagus_cuniculus.OryCun2.0/bowtie-indexes/Oryctolagus_cuniculus.OryCun2.0.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Oryctolagus_cuniculus.OryCun2.0/bowtie-indexes/Oryctolagus_cuniculus.OryCun2.0.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Oryctolagus_cuniculus-male-liver-H3K27Ac-ERR572126.50mers.unique
zcat Oryctolagus_cuniculus-male-liver-H3K27Ac-ERR572232.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Oryctolagus_cuniculus.OryCun2.0/bowtie-indexes/Oryctolagus_cuniculus.OryCun2.0.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Oryctolagus_cuniculus.OryCun2.0/bowtie-indexes/Oryctolagus_cuniculus.OryCun2.0.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Oryctolagus_cuniculus-male-liver-H3K27Ac-ERR572232.50mers.unique
zcat Oryctolagus_cuniculus-male-liver-H3K27Ac-ERR572222.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Oryctolagus_cuniculus.OryCun2.0/bowtie-indexes/Oryctolagus_cuniculus.OryCun2.0.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Oryctolagus_cuniculus.OryCun2.0/bowtie-indexes/Oryctolagus_cuniculus.OryCun2.0.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Oryctolagus_cuniculus-male-liver-H3K27Ac-ERR572222.50mers.unique
zcat Oryctolagus_cuniculus-male-liver-input-ERR572212.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Oryctolagus_cuniculus.OryCun2.0/bowtie-indexes/Oryctolagus_cuniculus.OryCun2.0.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Oryctolagus_cuniculus.OryCun2.0/bowtie-indexes/Oryctolagus_cuniculus.OryCun2.0.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Oryctolagus_cuniculus-male-liver-input-ERR572212.50mers.unique
zcat Oryctolagus_cuniculus-male-liver-input-ERR572238.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Oryctolagus_cuniculus.OryCun2.0/bowtie-indexes/Oryctolagus_cuniculus.OryCun2.0.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Oryctolagus_cuniculus.OryCun2.0/bowtie-indexes/Oryctolagus_cuniculus.OryCun2.0.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Oryctolagus_cuniculus-male-liver-input-ERR572238.50mers.unique
zcat Oryctolagus_cuniculus-male-liver-input-ERR572288.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Oryctolagus_cuniculus.OryCun2.0/bowtie-indexes/Oryctolagus_cuniculus.OryCun2.0.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Oryctolagus_cuniculus.OryCun2.0/bowtie-indexes/Oryctolagus_cuniculus.OryCun2.0.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Oryctolagus_cuniculus-male-liver-input-ERR572288.50mers.unique
zcat Tupaia_belangeri-male-liver-H3K4me3-ERR572196.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Tupaia_belangeri.TREESHREW/bowtie-indexes/Tupaia_belangeri.TREESHREW.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Tupaia_belangeri.TREESHREW/bowtie-indexes/Tupaia_belangeri.TREESHREW.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Tupaia_belangeri-male-liver-H3K4me3-ERR572196.50mers.unique
zcat Tupaia_belangeri-male-liver-H3K4me3-ERR572133.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Tupaia_belangeri.TREESHREW/bowtie-indexes/Tupaia_belangeri.TREESHREW.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Tupaia_belangeri.TREESHREW/bowtie-indexes/Tupaia_belangeri.TREESHREW.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Tupaia_belangeri-male-liver-H3K4me3-ERR572133.50mers.unique
zcat Tupaia_belangeri-female-liver-H3K4me3-ERR572298.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Tupaia_belangeri.TREESHREW/bowtie-indexes/Tupaia_belangeri.TREESHREW.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Tupaia_belangeri.TREESHREW/bowtie-indexes/Tupaia_belangeri.TREESHREW.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Tupaia_belangeri-female-liver-H3K4me3-ERR572298.50mers.unique
zcat Tupaia_belangeri-male-liver-H3K27Ac-ERR572256.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Tupaia_belangeri.TREESHREW/bowtie-indexes/Tupaia_belangeri.TREESHREW.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Tupaia_belangeri.TREESHREW/bowtie-indexes/Tupaia_belangeri.TREESHREW.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Tupaia_belangeri-male-liver-H3K27Ac-ERR572256.50mers.unique
zcat Tupaia_belangeri-male-liver-H3K27Ac-ERR572277.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Tupaia_belangeri.TREESHREW/bowtie-indexes/Tupaia_belangeri.TREESHREW.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Tupaia_belangeri.TREESHREW/bowtie-indexes/Tupaia_belangeri.TREESHREW.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Tupaia_belangeri-male-liver-H3K27Ac-ERR572277.50mers.unique
zcat Tupaia_belangeri-female-liver-H3K27Ac-ERR572198.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Tupaia_belangeri.TREESHREW/bowtie-indexes/Tupaia_belangeri.TREESHREW.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Tupaia_belangeri.TREESHREW/bowtie-indexes/Tupaia_belangeri.TREESHREW.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Tupaia_belangeri-female-liver-H3K27Ac-ERR572198.50mers.unique
zcat Tupaia_belangeri-male-liver-input-ERR572178.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Tupaia_belangeri.TREESHREW/bowtie-indexes/Tupaia_belangeri.TREESHREW.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Tupaia_belangeri.TREESHREW/bowtie-indexes/Tupaia_belangeri.TREESHREW.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Tupaia_belangeri-male-liver-input-ERR572178.50mers.unique
zcat Tupaia_belangeri-male-liver-input-ERR572268.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Tupaia_belangeri.TREESHREW/bowtie-indexes/Tupaia_belangeri.TREESHREW.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Tupaia_belangeri.TREESHREW/bowtie-indexes/Tupaia_belangeri.TREESHREW.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Tupaia_belangeri-male-liver-input-ERR572268.50mers.unique
zcat Tupaia_belangeri-female-liver-input-ERR572274.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Tupaia_belangeri.TREESHREW/bowtie-indexes/Tupaia_belangeri.TREESHREW.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Tupaia_belangeri.TREESHREW/bowtie-indexes/Tupaia_belangeri.TREESHREW.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Tupaia_belangeri-female-liver-input-ERR572274.50mers.unique
zcat Bos_taurus-male-liver-H3K4me3-ERR572160.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Bos_taurus.UMD3.1/bowtie-indexes/Bos_taurus.UMD3.1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Bos_taurus.UMD3.1/bowtie-indexes/Bos_taurus.UMD3.1.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Bos_taurus-male-liver-H3K4me3-ERR572160.50mers.unique
zcat Bos_taurus-male-liver-H3K4me3-ERR572137.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Bos_taurus.UMD3.1/bowtie-indexes/Bos_taurus.UMD3.1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Bos_taurus.UMD3.1/bowtie-indexes/Bos_taurus.UMD3.1.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Bos_taurus-male-liver-H3K4me3-ERR572137.50mers.unique
zcat Bos_taurus-male-liver-H3K4me3-ERR572243.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Bos_taurus.UMD3.1/bowtie-indexes/Bos_taurus.UMD3.1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Bos_taurus.UMD3.1/bowtie-indexes/Bos_taurus.UMD3.1.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Bos_taurus-male-liver-H3K4me3-ERR572243.50mers.unique
zcat Bos_taurus-male-liver-H3K4me3-ERR572180.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Bos_taurus.UMD3.1/bowtie-indexes/Bos_taurus.UMD3.1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Bos_taurus.UMD3.1/bowtie-indexes/Bos_taurus.UMD3.1.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Bos_taurus-male-liver-H3K4me3-ERR572180.50mers.unique
zcat Bos_taurus-male-liver-H3K27Ac-ERR572199.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Bos_taurus.UMD3.1/bowtie-indexes/Bos_taurus.UMD3.1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Bos_taurus.UMD3.1/bowtie-indexes/Bos_taurus.UMD3.1.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Bos_taurus-male-liver-H3K27Ac-ERR572199.50mers.unique
zcat Bos_taurus-male-liver-H3K27Ac-ERR572216.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Bos_taurus.UMD3.1/bowtie-indexes/Bos_taurus.UMD3.1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Bos_taurus.UMD3.1/bowtie-indexes/Bos_taurus.UMD3.1.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Bos_taurus-male-liver-H3K27Ac-ERR572216.50mers.unique
zcat Bos_taurus-male-liver-H3K27Ac-ERR572236.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Bos_taurus.UMD3.1/bowtie-indexes/Bos_taurus.UMD3.1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Bos_taurus.UMD3.1/bowtie-indexes/Bos_taurus.UMD3.1.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Bos_taurus-male-liver-H3K27Ac-ERR572236.50mers.unique
zcat Bos_taurus-male-liver-H3K27Ac-ERR572139.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Bos_taurus.UMD3.1/bowtie-indexes/Bos_taurus.UMD3.1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Bos_taurus.UMD3.1/bowtie-indexes/Bos_taurus.UMD3.1.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Bos_taurus-male-liver-H3K27Ac-ERR572139.50mers.unique
zcat Bos_taurus-male-liver-input-ERR572283.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Bos_taurus.UMD3.1/bowtie-indexes/Bos_taurus.UMD3.1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Bos_taurus.UMD3.1/bowtie-indexes/Bos_taurus.UMD3.1.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Bos_taurus-male-liver-input-ERR572283.50mers.unique
zcat Bos_taurus-male-liver-input-ERR572271.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Bos_taurus.UMD3.1/bowtie-indexes/Bos_taurus.UMD3.1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Bos_taurus.UMD3.1/bowtie-indexes/Bos_taurus.UMD3.1.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Bos_taurus-male-liver-input-ERR572271.50mers.unique
zcat Bos_taurus-male-liver-input-ERR572132.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Bos_taurus.UMD3.1/bowtie-indexes/Bos_taurus.UMD3.1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Bos_taurus.UMD3.1/bowtie-indexes/Bos_taurus.UMD3.1.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Bos_taurus-male-liver-input-ERR572132.50mers.unique
zcat Bos_taurus-male-liver-input-ERR572289.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Bos_taurus.UMD3.1/bowtie-indexes/Bos_taurus.UMD3.1.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Bos_taurus.UMD3.1/bowtie-indexes/Bos_taurus.UMD3.1.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Bos_taurus-male-liver-input-ERR572289.50mers.unique
zcat Sus_scrofa-male-liver-H3K4me3-ERR572292.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Sus_scrofa-Sscrofa10.2_susScr3/bowtie-indexes/GCA_000003025.4_Sscrofa10.2_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Sus_scrofa-Sscrofa10.2_susScr3/bowtie-indexes/GCA_000003025.4_Sscrofa10.2_genomic.fa - | ~/programs/samtools-0.1.18/samtools sort - Sus_scrofa-male-liver-H3K4me3-ERR572292.50mers.unique
zcat Sus_scrofa-male-liver-H3K4me3-ERR572197.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Sus_scrofa-Sscrofa10.2_susScr3/bowtie-indexes/GCA_000003025.4_Sscrofa10.2_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Sus_scrofa-Sscrofa10.2_susScr3/bowtie-indexes/GCA_000003025.4_Sscrofa10.2_genomic.fa - | ~/programs/samtools-0.1.18/samtools sort - Sus_scrofa-male-liver-H3K4me3-ERR572197.50mers.unique
zcat Sus_scrofa-male-liver-H3K4me3-ERR572167.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Sus_scrofa-Sscrofa10.2_susScr3/bowtie-indexes/GCA_000003025.4_Sscrofa10.2_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Sus_scrofa-Sscrofa10.2_susScr3/bowtie-indexes/GCA_000003025.4_Sscrofa10.2_genomic.fa - | ~/programs/samtools-0.1.18/samtools sort - Sus_scrofa-male-liver-H3K4me3-ERR572167.50mers.unique
zcat Sus_scrofa-male-liver-H3K27Ac-ERR572204.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Sus_scrofa-Sscrofa10.2_susScr3/bowtie-indexes/GCA_000003025.4_Sscrofa10.2_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Sus_scrofa-Sscrofa10.2_susScr3/bowtie-indexes/GCA_000003025.4_Sscrofa10.2_genomic.fa - | ~/programs/samtools-0.1.18/samtools sort - Sus_scrofa-male-liver-H3K27Ac-ERR572204.50mers.unique
zcat Sus_scrofa-male-liver-H3K27Ac-ERR572261.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Sus_scrofa-Sscrofa10.2_susScr3/bowtie-indexes/GCA_000003025.4_Sscrofa10.2_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Sus_scrofa-Sscrofa10.2_susScr3/bowtie-indexes/GCA_000003025.4_Sscrofa10.2_genomic.fa - | ~/programs/samtools-0.1.18/samtools sort - Sus_scrofa-male-liver-H3K27Ac-ERR572261.50mers.unique
zcat Sus_scrofa-male-liver-H3K27Ac-ERR572214.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Sus_scrofa-Sscrofa10.2_susScr3/bowtie-indexes/GCA_000003025.4_Sscrofa10.2_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Sus_scrofa-Sscrofa10.2_susScr3/bowtie-indexes/GCA_000003025.4_Sscrofa10.2_genomic.fa - | ~/programs/samtools-0.1.18/samtools sort - Sus_scrofa-male-liver-H3K27Ac-ERR572214.50mers.unique
zcat Sus_scrofa-male-liver-input-ERR572294.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Sus_scrofa-Sscrofa10.2_susScr3/bowtie-indexes/GCA_000003025.4_Sscrofa10.2_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Sus_scrofa-Sscrofa10.2_susScr3/bowtie-indexes/GCA_000003025.4_Sscrofa10.2_genomic.fa - | ~/programs/samtools-0.1.18/samtools sort - Sus_scrofa-male-liver-input-ERR572294.50mers.unique
zcat Sus_scrofa-male-liver-input-ERR572157.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Sus_scrofa-Sscrofa10.2_susScr3/bowtie-indexes/GCA_000003025.4_Sscrofa10.2_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Sus_scrofa-Sscrofa10.2_susScr3/bowtie-indexes/GCA_000003025.4_Sscrofa10.2_genomic.fa - | ~/programs/samtools-0.1.18/samtools sort - Sus_scrofa-male-liver-input-ERR572157.50mers.unique
zcat Sus_scrofa-male-liver-input-ERR572138.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Sus_scrofa-Sscrofa10.2_susScr3/bowtie-indexes/GCA_000003025.4_Sscrofa10.2_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Sus_scrofa-Sscrofa10.2_susScr3/bowtie-indexes/GCA_000003025.4_Sscrofa10.2_genomic.fa - | ~/programs/samtools-0.1.18/samtools sort - Sus_scrofa-male-liver-input-ERR572138.50mers.unique
zcat Canis_familiaris-male-liver-H3K4me3-ERR572260.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/canFam3/bowtie-indexes/canFam3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/canFam3/bowtie-indexes/canFam3.fa - | ~/programs/samtools-0.1.18/samtools sort - Canis_familiaris-male-liver-H3K4me3-ERR572260.50mers.unique
zcat Canis_familiaris-male-liver-H3K4me3-ERR572190.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/canFam3/bowtie-indexes/canFam3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/canFam3/bowtie-indexes/canFam3.fa - | ~/programs/samtools-0.1.18/samtools sort - Canis_familiaris-male-liver-H3K4me3-ERR572190.50mers.unique
zcat Canis_familiaris-male-liver-H3K4me3-ERR572299.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/canFam3/bowtie-indexes/canFam3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/canFam3/bowtie-indexes/canFam3.fa - | ~/programs/samtools-0.1.18/samtools sort - Canis_familiaris-male-liver-H3K4me3-ERR572299.50mers.unique
zcat Canis_familiaris-male-liver-H3K27Ac-ERR572253.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/canFam3/bowtie-indexes/canFam3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/canFam3/bowtie-indexes/canFam3.fa - | ~/programs/samtools-0.1.18/samtools sort - Canis_familiaris-male-liver-H3K27Ac-ERR572253.50mers.unique
zcat Canis_familiaris-male-liver-H3K27Ac-ERR572282.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/canFam3/bowtie-indexes/canFam3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/canFam3/bowtie-indexes/canFam3.fa - | ~/programs/samtools-0.1.18/samtools sort - Canis_familiaris-male-liver-H3K27Ac-ERR572282.50mers.unique
zcat Canis_familiaris-male-liver-H3K27Ac-ERR572275.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/canFam3/bowtie-indexes/canFam3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/canFam3/bowtie-indexes/canFam3.fa - | ~/programs/samtools-0.1.18/samtools sort - Canis_familiaris-male-liver-H3K27Ac-ERR572275.50mers.unique
zcat Canis_familiaris-male-liver-input-ERR572259.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/canFam3/bowtie-indexes/canFam3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/canFam3/bowtie-indexes/canFam3.fa - | ~/programs/samtools-0.1.18/samtools sort - Canis_familiaris-male-liver-input-ERR572259.50mers.unique
zcat Canis_familiaris-male-liver-input-ERR572207.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/canFam3/bowtie-indexes/canFam3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/canFam3/bowtie-indexes/canFam3.fa - | ~/programs/samtools-0.1.18/samtools sort - Canis_familiaris-male-liver-input-ERR572207.50mers.unique
zcat Canis_familiaris-male-liver-input-ERR572210.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/canFam3/bowtie-indexes/canFam3 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/canFam3/bowtie-indexes/canFam3.fa - | ~/programs/samtools-0.1.18/samtools sort - Canis_familiaris-male-liver-input-ERR572210.50mers.unique
zcat Felis_catus-female-liver-H3K4me3-ERR572163.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/felCat8/bowtie-indexes/felCat8 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/felCat8/bowtie-indexes/felCat8.fa - | ~/programs/samtools-0.1.18/samtools sort - Felis_catus-female-liver-H3K4me3-ERR572163.50mers.unique
zcat Felis_catus-female-liver-H3K4me3-ERR572244.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/felCat8/bowtie-indexes/felCat8 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/felCat8/bowtie-indexes/felCat8.fa - | ~/programs/samtools-0.1.18/samtools sort - Felis_catus-female-liver-H3K4me3-ERR572244.50mers.unique
zcat Felis_catus-female-liver-H3K27Ac-ERR572257.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/felCat8/bowtie-indexes/felCat8 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/felCat8/bowtie-indexes/felCat8.fa - | ~/programs/samtools-0.1.18/samtools sort - Felis_catus-female-liver-H3K27Ac-ERR572257.50mers.unique
zcat Felis_catus-female-liver-H3K27Ac-ERR572171.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/felCat8/bowtie-indexes/felCat8 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/felCat8/bowtie-indexes/felCat8.fa - | ~/programs/samtools-0.1.18/samtools sort - Felis_catus-female-liver-H3K27Ac-ERR572171.50mers.unique
zcat Felis_catus-female-liver-input-ERR572235.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/felCat8/bowtie-indexes/felCat8 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/felCat8/bowtie-indexes/felCat8.fa - | ~/programs/samtools-0.1.18/samtools sort - Felis_catus-female-liver-input-ERR572235.50mers.unique
zcat Felis_catus-female-liver-input-ERR572152.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/felCat8/bowtie-indexes/felCat8 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/felCat8/bowtie-indexes/felCat8.fa - | ~/programs/samtools-0.1.18/samtools sort - Felis_catus-female-liver-input-ERR572152.50mers.unique
zcat Mustela_putorius_furo-male-liver-H3K4me3-ERR572130.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Mustela_putorius_furo.MusPutFur1.0/bowtie-indexes/Mustela_putorius_furo.MusPutFur1.0.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Mustela_putorius_furo.MusPutFur1.0/bowtie-indexes/Mustela_putorius_furo.MusPutFur1.0.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Mustela_putorius_furo-male-liver-H3K4me3-ERR572130.50mers.unique
zcat Mustela_putorius_furo-male-liver-H3K4me3-ERR572191.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Mustela_putorius_furo.MusPutFur1.0/bowtie-indexes/Mustela_putorius_furo.MusPutFur1.0.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Mustela_putorius_furo.MusPutFur1.0/bowtie-indexes/Mustela_putorius_furo.MusPutFur1.0.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Mustela_putorius_furo-male-liver-H3K4me3-ERR572191.50mers.unique
zcat Mustela_putorius_furo-male-liver-H3K4me3-ERR572224.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Mustela_putorius_furo.MusPutFur1.0/bowtie-indexes/Mustela_putorius_furo.MusPutFur1.0.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Mustela_putorius_furo.MusPutFur1.0/bowtie-indexes/Mustela_putorius_furo.MusPutFur1.0.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Mustela_putorius_furo-male-liver-H3K4me3-ERR572224.50mers.unique
zcat Mustela_putorius_furo-male-liver-H3K27Ac-ERR572131.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Mustela_putorius_furo.MusPutFur1.0/bowtie-indexes/Mustela_putorius_furo.MusPutFur1.0.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Mustela_putorius_furo.MusPutFur1.0/bowtie-indexes/Mustela_putorius_furo.MusPutFur1.0.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Mustela_putorius_furo-male-liver-H3K27Ac-ERR572131.50mers.unique
zcat Mustela_putorius_furo-male-liver-H3K27Ac-ERR572200.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Mustela_putorius_furo.MusPutFur1.0/bowtie-indexes/Mustela_putorius_furo.MusPutFur1.0.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Mustela_putorius_furo.MusPutFur1.0/bowtie-indexes/Mustela_putorius_furo.MusPutFur1.0.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Mustela_putorius_furo-male-liver-H3K27Ac-ERR572200.50mers.unique
zcat Mustela_putorius_furo-male-liver-H3K27Ac-ERR572293.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Mustela_putorius_furo.MusPutFur1.0/bowtie-indexes/Mustela_putorius_furo.MusPutFur1.0.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Mustela_putorius_furo.MusPutFur1.0/bowtie-indexes/Mustela_putorius_furo.MusPutFur1.0.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Mustela_putorius_furo-male-liver-H3K27Ac-ERR572293.50mers.unique
zcat Mustela_putorius_furo-male-liver-input-ERR572164.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Mustela_putorius_furo.MusPutFur1.0/bowtie-indexes/Mustela_putorius_furo.MusPutFur1.0.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Mustela_putorius_furo.MusPutFur1.0/bowtie-indexes/Mustela_putorius_furo.MusPutFur1.0.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Mustela_putorius_furo-male-liver-input-ERR572164.50mers.unique
zcat Mustela_putorius_furo-male-liver-input-ERR572217.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Mustela_putorius_furo.MusPutFur1.0/bowtie-indexes/Mustela_putorius_furo.MusPutFur1.0.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Mustela_putorius_furo.MusPutFur1.0/bowtie-indexes/Mustela_putorius_furo.MusPutFur1.0.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Mustela_putorius_furo-male-liver-input-ERR572217.50mers.unique
zcat Mustela_putorius_furo-male-liver-input-ERR572254.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Mustela_putorius_furo.MusPutFur1.0/bowtie-indexes/Mustela_putorius_furo.MusPutFur1.0.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Mustela_putorius_furo.MusPutFur1.0/bowtie-indexes/Mustela_putorius_furo.MusPutFur1.0.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Mustela_putorius_furo-male-liver-input-ERR572254.50mers.unique
zcat Monodelphis_domestica-male-liver-H3K4me3-ERR572165.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Monodelphis_domestica/bowtie-indexes/Monodelphis_domestica.BROADO5.73 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Monodelphis_domestica/bowtie-indexes/Monodelphis_domestica.BROADO5.73.fa - | ~/programs/samtools-0.1.18/samtools sort - Monodelphis_domestica-male-liver-H3K4me3-ERR572165.50mers.unique
zcat Monodelphis_domestica-male-liver-H3K4me3-ERR572135.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Monodelphis_domestica/bowtie-indexes/Monodelphis_domestica.BROADO5.73 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Monodelphis_domestica/bowtie-indexes/Monodelphis_domestica.BROADO5.73.fa - | ~/programs/samtools-0.1.18/samtools sort - Monodelphis_domestica-male-liver-H3K4me3-ERR572135.50mers.unique
zcat Monodelphis_domestica-male-liver-H3K4me3-ERR572252.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Monodelphis_domestica/bowtie-indexes/Monodelphis_domestica.BROADO5.73 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Monodelphis_domestica/bowtie-indexes/Monodelphis_domestica.BROADO5.73.fa - | ~/programs/samtools-0.1.18/samtools sort - Monodelphis_domestica-male-liver-H3K4me3-ERR572252.50mers.unique
zcat Monodelphis_domestica-male-liver-H3K27Ac-ERR572161.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Monodelphis_domestica/bowtie-indexes/Monodelphis_domestica.BROADO5.73 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Monodelphis_domestica/bowtie-indexes/Monodelphis_domestica.BROADO5.73.fa - | ~/programs/samtools-0.1.18/samtools sort - Monodelphis_domestica-male-liver-H3K27Ac-ERR572161.50mers.unique
zcat Monodelphis_domestica-male-liver-H3K27Ac-ERR572297.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Monodelphis_domestica/bowtie-indexes/Monodelphis_domestica.BROADO5.73 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Monodelphis_domestica/bowtie-indexes/Monodelphis_domestica.BROADO5.73.fa - | ~/programs/samtools-0.1.18/samtools sort - Monodelphis_domestica-male-liver-H3K27Ac-ERR572297.50mers.unique
zcat Monodelphis_domestica-male-liver-H3K27Ac-ERR572158.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Monodelphis_domestica/bowtie-indexes/Monodelphis_domestica.BROADO5.73 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Monodelphis_domestica/bowtie-indexes/Monodelphis_domestica.BROADO5.73.fa - | ~/programs/samtools-0.1.18/samtools sort - Monodelphis_domestica-male-liver-H3K27Ac-ERR572158.50mers.unique
zcat Monodelphis_domestica-male-liver-input-ERR572128.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Monodelphis_domestica/bowtie-indexes/Monodelphis_domestica.BROADO5.73 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Monodelphis_domestica/bowtie-indexes/Monodelphis_domestica.BROADO5.73.fa - | ~/programs/samtools-0.1.18/samtools sort - Monodelphis_domestica-male-liver-input-ERR572128.50mers.unique
zcat Monodelphis_domestica-male-liver-input-ERR572193.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Monodelphis_domestica/bowtie-indexes/Monodelphis_domestica.BROADO5.73 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Monodelphis_domestica/bowtie-indexes/Monodelphis_domestica.BROADO5.73.fa - | ~/programs/samtools-0.1.18/samtools sort - Monodelphis_domestica-male-liver-input-ERR572193.50mers.unique
zcat Monodelphis_domestica-male-liver-input-ERR572278.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Monodelphis_domestica/bowtie-indexes/Monodelphis_domestica.BROADO5.73 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Monodelphis_domestica/bowtie-indexes/Monodelphis_domestica.BROADO5.73.fa - | ~/programs/samtools-0.1.18/samtools sort - Monodelphis_domestica-male-liver-input-ERR572278.50mers.unique
zcat Sarcophilus_harrisii-female-liver-H3K4me3-ERR572296.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Sarcophilus_harrisii.DEVIL7.0/bowtie-indexes/Sarcophilus_harrisii.DEVIL7.0.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Sarcophilus_harrisii.DEVIL7.0/bowtie-indexes/Sarcophilus_harrisii.DEVIL7.0.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Sarcophilus_harrisii-female-liver-H3K4me3-ERR572296.50mers.unique
zcat Sarcophilus_harrisii-male-liver-H3K4me3-ERR572134.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Sarcophilus_harrisii.DEVIL7.0/bowtie-indexes/Sarcophilus_harrisii.DEVIL7.0.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Sarcophilus_harrisii.DEVIL7.0/bowtie-indexes/Sarcophilus_harrisii.DEVIL7.0.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Sarcophilus_harrisii-male-liver-H3K4me3-ERR572134.50mers.unique
zcat Sarcophilus_harrisii-female-liver-H3K27Ac-ERR572147.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Sarcophilus_harrisii.DEVIL7.0/bowtie-indexes/Sarcophilus_harrisii.DEVIL7.0.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Sarcophilus_harrisii.DEVIL7.0/bowtie-indexes/Sarcophilus_harrisii.DEVIL7.0.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Sarcophilus_harrisii-female-liver-H3K27Ac-ERR572147.50mers.unique
zcat Sarcophilus_harrisii-male-liver-H3K27Ac-ERR572156.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Sarcophilus_harrisii.DEVIL7.0/bowtie-indexes/Sarcophilus_harrisii.DEVIL7.0.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Sarcophilus_harrisii.DEVIL7.0/bowtie-indexes/Sarcophilus_harrisii.DEVIL7.0.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Sarcophilus_harrisii-male-liver-H3K27Ac-ERR572156.50mers.unique
zcat Sarcophilus_harrisii-female-liver-input-ERR572237.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Sarcophilus_harrisii.DEVIL7.0/bowtie-indexes/Sarcophilus_harrisii.DEVIL7.0.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Sarcophilus_harrisii.DEVIL7.0/bowtie-indexes/Sarcophilus_harrisii.DEVIL7.0.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Sarcophilus_harrisii-female-liver-input-ERR572237.50mers.unique
zcat Sarcophilus_harrisii-male-liver-input-ERR572194.fastq.gz | python ~/code/trimfastq.py - 50 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Metazoa/Chordates/Sarcophilus_harrisii.DEVIL7.0/bowtie-indexes/Sarcophilus_harrisii.DEVIL7.0.dna.toplevel -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Metazoa/Chordates/Sarcophilus_harrisii.DEVIL7.0/bowtie-indexes/Sarcophilus_harrisii.DEVIL7.0.dna.toplevel.fa - | ~/programs/samtools-0.1.18/samtools sort - Sarcophilus_harrisii-male-liver-input-ERR572194.50mers.unique