cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/65/; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR943786 | python /N/dc2/projects/marinovg/code/trimfastq.py - 35 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10 -p 16 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/TAIR10/sequence/TAIR10.fa - | samtools sort - prr7-3_Input_ExpI-GSM1196645.36mers.unique
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/65/; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR943787 | python /N/dc2/projects/marinovg/code/trimfastq.py - 35 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10 -p 16 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/TAIR10/sequence/TAIR10.fa - | samtools sort - prr7-3_IP_ExpI-GSM1196646.36mers.unique
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/65/; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR943788 | python /N/dc2/projects/marinovg/code/trimfastq.py - 35 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10 -p 16 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/TAIR10/sequence/TAIR10.fa - | samtools sort - prr7-3_PRR7_HA-PRR7_151_Input_ExpI-GSM1196647.36mers.unique
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/65/; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR943789 | python /N/dc2/projects/marinovg/code/trimfastq.py - 35 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10 -p 16 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/TAIR10/sequence/TAIR10.fa - | samtools sort - prr7-3_PRR7_HA-PRR7_151_IP_ExpI-GSM1196648.36mers.unique
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/65/; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR943790 | python /N/dc2/projects/marinovg/code/trimfastq.py - 35 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10 -p 16 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/TAIR10/sequence/TAIR10.fa - | samtools sort - prr7-3_PRR7_HA-PRR7_151_IP_ExpII-GSM1196649.36mers.unique
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/65/; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR943791 | python /N/dc2/projects/marinovg/code/trimfastq.py - 35 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/TAIR10/bowtie-indexes/TAIR10 -p 16 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/TAIR10/sequence/TAIR10.fa - | samtools sort - prr7-3_IP_ExpII-GSM1196650.36mers.unique