/N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa/29CHIP_Input-GSM1035301.sra | python /N/dc2/projects/marinovg/code/trimfastq.py - 36 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Land_plants/Oryza_sativa/bowtie-indexes/Oryza_sativa.MSU6 -p 16 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Land_plants/Oryza_sativa/sequence/Oryza_sativa.MSU6.fa - | samtools sort - /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa/29CHIP_Input-GSM1035301.36mers.unique
/N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa/29CHIP_mock-GSM1035302.sra | python /N/dc2/projects/marinovg/code/trimfastq.py - 36 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Land_plants/Oryza_sativa/bowtie-indexes/Oryza_sativa.MSU6 -p 16 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Land_plants/Oryza_sativa/sequence/Oryza_sativa.MSU6.fa - | samtools sort - /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa/29CHIP_mock-GSM1035302.36mers.unique
/N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa/MADS29-CHIP_IPsample-GSM1035300.sra | python /N/dc2/projects/marinovg/code/trimfastq.py - 36 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Land_plants/Oryza_sativa/bowtie-indexes/Oryza_sativa.MSU6 -p 16 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Land_plants/Oryza_sativa/sequence/Oryza_sativa.MSU6.fa - | samtools sort - /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa/MADS29-CHIP_IPsample-GSM1035300.36mers.unique