cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/47-Sulfolobus_solfataricus_98_2_uid167998; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1552717 | python /N/dc2/projects/marinovg/code/trimfastq.py - 36 -trim5 8 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Archaea/Crenarchaeota/Sulfolobus_solfataricus_98_2_uid167998/bowtie-indexes/NC_017274 -p 16 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Archaea/Crenarchaeota/Sulfolobus_solfataricus_98_2_uid167998/bowtie-indexes/NC_017274.fa - | samtools sort - MerR+Hg-ChIPSeq-GSM1480363.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/47-Sulfolobus_solfataricus_98_2_uid167998; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1552718 | python /N/dc2/projects/marinovg/code/trimfastq.py - 36 -trim5 8 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Archaea/Crenarchaeota/Sulfolobus_solfataricus_98_2_uid167998/bowtie-indexes/NC_017274 -p 16 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Archaea/Crenarchaeota/Sulfolobus_solfataricus_98_2_uid167998/bowtie-indexes/NC_017274.fa - | samtools sort - MerR-Hg-ChIPSeq-GSM1480364.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/47-Sulfolobus_solfataricus_98_2_uid167998; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1552719 | python /N/dc2/projects/marinovg/code/trimfastq.py - 36 -trim5 8 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Archaea/Crenarchaeota/Sulfolobus_solfataricus_98_2_uid167998/bowtie-indexes/NC_017274 -p 16 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Archaea/Crenarchaeota/Sulfolobus_solfataricus_98_2_uid167998/bowtie-indexes/NC_017274.fa - | samtools sort - MerR-Hg-WCE-GSM1480365.36mers.unique