cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/25-Rhodobacter_sphaeroides; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1448455 | 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/Bacteria/Rhodobacter_sphaeroides_2.4.1-ASM1290v2/bowtie-indexes/GCA_000012905.2_ASM1290v2_genomic -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Rhodobacter_sphaeroides_2.4.1-ASM1290v2/bowtie-indexes/GCA_000012905.2_ASM1290v2_genomic.fa - | samtools sort - PrrA_3xMyc_ChIP_Seq-GSM1417292.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/25-Rhodobacter_sphaeroides; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1448456 | 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/Bacteria/Rhodobacter_sphaeroides_2.4.1-ASM1290v2/bowtie-indexes/GCA_000012905.2_ASM1290v2_genomic -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Rhodobacter_sphaeroides_2.4.1-ASM1290v2/bowtie-indexes/GCA_000012905.2_ASM1290v2_genomic.fa - | samtools sort - CrpK_3xMyc_ChIP_Seq-GSM1417293.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/25-Rhodobacter_sphaeroides; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1448457 | 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/Bacteria/Rhodobacter_sphaeroides_2.4.1-ASM1290v2/bowtie-indexes/GCA_000012905.2_ASM1290v2_genomic -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Rhodobacter_sphaeroides_2.4.1-ASM1290v2/bowtie-indexes/GCA_000012905.2_ASM1290v2_genomic.fa - | samtools sort - RSP_2888_3xMyc_ChIP_Seq_Rep1-GSM1417294.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/25-Rhodobacter_sphaeroides; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1448458 | 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/Bacteria/Rhodobacter_sphaeroides_2.4.1-ASM1290v2/bowtie-indexes/GCA_000012905.2_ASM1290v2_genomic -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Rhodobacter_sphaeroides_2.4.1-ASM1290v2/bowtie-indexes/GCA_000012905.2_ASM1290v2_genomic.fa - | samtools sort - RSP_2888_3xMyc_ChIP_Seq_Rep2-GSM1417295.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/25-Rhodobacter_sphaeroides; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1448459 | 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/Bacteria/Rhodobacter_sphaeroides_2.4.1-ASM1290v2/bowtie-indexes/GCA_000012905.2_ASM1290v2_genomic -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Rhodobacter_sphaeroides_2.4.1-ASM1290v2/bowtie-indexes/GCA_000012905.2_ASM1290v2_genomic.fa - | samtools sort - FnrL_ChIP_Seq_Rep1-GSM1417296.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/25-Rhodobacter_sphaeroides; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1448460 | 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/Bacteria/Rhodobacter_sphaeroides_2.4.1-ASM1290v2/bowtie-indexes/GCA_000012905.2_ASM1290v2_genomic -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Rhodobacter_sphaeroides_2.4.1-ASM1290v2/bowtie-indexes/GCA_000012905.2_ASM1290v2_genomic.fa - | samtools sort - FnrL_ChIP_Seq_Rep2-GSM1417297.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/25-Rhodobacter_sphaeroides; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1448461 | 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/Bacteria/Rhodobacter_sphaeroides_2.4.1-ASM1290v2/bowtie-indexes/GCA_000012905.2_ASM1290v2_genomic -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Rhodobacter_sphaeroides_2.4.1-ASM1290v2/bowtie-indexes/GCA_000012905.2_ASM1290v2_genomic.fa - | samtools sort - FnrL_ChIP_Seq_Rep3-GSM1417298.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/25-Rhodobacter_sphaeroides; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1448462 | 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/Bacteria/Rhodobacter_sphaeroides_2.4.1-ASM1290v2/bowtie-indexes/GCA_000012905.2_ASM1290v2_genomic -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Rhodobacter_sphaeroides_2.4.1-ASM1290v2/bowtie-indexes/GCA_000012905.2_ASM1290v2_genomic.fa - | samtools sort - FnrL_Control_ChIP-GSM1417299.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/25-Rhodobacter_sphaeroides; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1448463 | 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/Bacteria/Rhodobacter_sphaeroides_2.4.1-ASM1290v2/bowtie-indexes/GCA_000012905.2_ASM1290v2_genomic -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Rhodobacter_sphaeroides_2.4.1-ASM1290v2/bowtie-indexes/GCA_000012905.2_ASM1290v2_genomic.fa - | samtools sort - Input_DNA-GSM1417300.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/25-Rhodobacter_sphaeroides; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1448464 | 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/Bacteria/Rhodobacter_sphaeroides_2.4.1-ASM1290v2/bowtie-indexes/GCA_000012905.2_ASM1290v2_genomic -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Rhodobacter_sphaeroides_2.4.1-ASM1290v2/bowtie-indexes/GCA_000012905.2_ASM1290v2_genomic.fa - | samtools sort - Input_DNA_pairedEnd-GSM1417301.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/25-Rhodobacter_sphaeroides; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1448465 | 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/Bacteria/Rhodobacter_sphaeroides_2.4.1-ASM1290v2/bowtie-indexes/GCA_000012905.2_ASM1290v2_genomic -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Rhodobacter_sphaeroides_2.4.1-ASM1290v2/bowtie-indexes/GCA_000012905.2_ASM1290v2_genomic.fa - | samtools sort - Myc_Control_ChIP_seq_Aero-GSM1417302.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/25-Rhodobacter_sphaeroides; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1448466 | 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/Bacteria/Rhodobacter_sphaeroides_2.4.1-ASM1290v2/bowtie-indexes/GCA_000012905.2_ASM1290v2_genomic -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Rhodobacter_sphaeroides_2.4.1-ASM1290v2/bowtie-indexes/GCA_000012905.2_ASM1290v2_genomic.fa - | samtools sort - Myc_Control_ChIP_seq_Photo-GSM1417303.36mers.unique