zcat WT_mock_ChIP-GSM2837359/*_1.fastq.gz | python ~/code/trimfastq.py - 33 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/TAIR10/bowtie-indexes/chrM+chloroplast -p 8 -v 2 -k 3 -m 2 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/TAIR10/sequence/TAIR10.fa - | ~/programs/samtools-0.1.18/samtools sort - WT_mock_ChIP-GSM2837359/all.1x36mers.chrM+chloroplast.k3m2
zcat WT_mock_ChIP-GSM2837359/*_1.fastq.gz | python ~/code/trimfastq.py - 33 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/TAIR10/sequence/TAIR10.fa - | ~/programs/samtools-0.1.18/samtools sort - WT_mock_ChIP-GSM2837359/all.1x36mers.TAIR10.unique
zcat SOG1-Myc_zeocin_ChIP-GSM2837360/*_1.fastq.gz | python ~/code/trimfastq.py - 33 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/TAIR10/bowtie-indexes/chrM+chloroplast -p 8 -v 2 -k 3 -m 2 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/TAIR10/sequence/TAIR10.fa - | ~/programs/samtools-0.1.18/samtools sort - SOG1-Myc_zeocin_ChIP-GSM2837360/all.1x36mers.chrM+chloroplast.k3m2
zcat SOG1-Myc_zeocin_ChIP-GSM2837360/*_1.fastq.gz | python ~/code/trimfastq.py - 33 -stdout | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/TAIR10/bowtie-indexes/TAIR10 -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/TAIR10/sequence/TAIR10.fa - | ~/programs/samtools-0.1.18/samtools sort - SOG1-Myc_zeocin_ChIP-GSM2837360/all.1x36mers.TAIR10.unique