cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/32-Francisella_tularensis_holarctica_LVS_uid58595; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1827598 | 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/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880.fa - | samtools sort - LVS_mock-rep1.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/32-Francisella_tularensis_holarctica_LVS_uid58595; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1827597 | 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/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880.fa - | samtools sort - LVS_mock-rep2.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/32-Francisella_tularensis_holarctica_LVS_uid58595; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1827596 | 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/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880.fa - | samtools sort - LVS_mock-rep3.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/32-Francisella_tularensis_holarctica_LVS_uid58595; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1827626 | 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/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880.fa - | samtools sort - LVS_delta_pigR_delta_mglA_pF-PigR-V-rep1.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/32-Francisella_tularensis_holarctica_LVS_uid58595; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1827625 | 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/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880.fa - | samtools sort - LVS_delta_pigR_delta_mglA_pF-PigR-V-rep2.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/32-Francisella_tularensis_holarctica_LVS_uid58595; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1827624 | 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/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880.fa - | samtools sort - LVS_delta_pigR_pF2-PigR-V-rep1.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/32-Francisella_tularensis_holarctica_LVS_uid58595; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1827623 | 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/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880.fa - | samtools sort - LVS_delta_pigR_pF2-PigR-V-rep2.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/32-Francisella_tularensis_holarctica_LVS_uid58595; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1827622 | 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/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880.fa - | samtools sort - LVS_delta_pigR_pF2-PigR-V-rep3.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/32-Francisella_tularensis_holarctica_LVS_uid58595; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1827621 | 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/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880.fa - | samtools sort - LVS_pF_lacking_any_VSV-G_tagged_protein:_Sample_LVS_pF-rep1.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/32-Francisella_tularensis_holarctica_LVS_uid58595; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1827620 | 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/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880.fa - | samtools sort - LVS_pF_lacking_any_VSV-G_tagged_protein:_Sample_LVS_pF-rep2.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/32-Francisella_tularensis_holarctica_LVS_uid58595; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1827619 | 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/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880.fa - | samtools sort - LVS_HipB-V-rep1.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/32-Francisella_tularensis_holarctica_LVS_uid58595; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1827618 | 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/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880.fa - | samtools sort - LVS_HipB-V-rep2.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/32-Francisella_tularensis_holarctica_LVS_uid58595; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1827617 | 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/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880.fa - | samtools sort - LVS_HipB-V-rep3.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/32-Francisella_tularensis_holarctica_LVS_uid58595; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1827616 | 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/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880.fa - | samtools sort - LVS_PigR-V-rep1.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/32-Francisella_tularensis_holarctica_LVS_uid58595; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1827615 | 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/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880.fa - | samtools sort - LVS_PigR-V-rep2.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/32-Francisella_tularensis_holarctica_LVS_uid58595; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1827614 | 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/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880.fa - | samtools sort - LVS_PigR-V-rep3.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/32-Francisella_tularensis_holarctica_LVS_uid58595; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1827613 | 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/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880.fa - | samtools sort - LVS_SspA-V-rep1.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/32-Francisella_tularensis_holarctica_LVS_uid58595; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1827612 | 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/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880.fa - | samtools sort - LVS_SspA-V-rep2.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/32-Francisella_tularensis_holarctica_LVS_uid58595; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1827611 | 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/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880.fa - | samtools sort - LVS_SspA-V-rep3.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/32-Francisella_tularensis_holarctica_LVS_uid58595; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1827610 | 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/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880.fa - | samtools sort - LVS_MglA-TAP-rep1.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/32-Francisella_tularensis_holarctica_LVS_uid58595; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1827609 | 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/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880.fa - | samtools sort - LVS_MglA-TAP-rep2.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/32-Francisella_tularensis_holarctica_LVS_uid58595; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1827608 | 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/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880.fa - | samtools sort - LVS_MglA-TAP-rep3.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/32-Francisella_tularensis_holarctica_LVS_uid58595; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1827607 | 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/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880.fa - | samtools sort - LVS_Sigma32-V-rep1.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/32-Francisella_tularensis_holarctica_LVS_uid58595; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1827606 | 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/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880.fa - | samtools sort - LVS_Sigma32-V-rep2.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/32-Francisella_tularensis_holarctica_LVS_uid58595; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1827605 | 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/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880.fa - | samtools sort - LVS_Sigma32-V-rep3.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/32-Francisella_tularensis_holarctica_LVS_uid58595; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1827604 | 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/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880.fa - | samtools sort - LVS_Sigma70-V-rep1.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/32-Francisella_tularensis_holarctica_LVS_uid58595; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1827603 | 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/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880.fa - | samtools sort - LVS_Sigma70-V-rep2.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/32-Francisella_tularensis_holarctica_LVS_uid58595; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1827602 | 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/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880.fa - | samtools sort - LVS_Sigma70-V-rep3.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/32-Francisella_tularensis_holarctica_LVS_uid58595; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1827601 | 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/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880.fa - | samtools sort - LVS_Sigma70-V-rep4.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/32-Francisella_tularensis_holarctica_LVS_uid58595; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1827600 | 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/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880.fa - | samtools sort - LVS_Beta_prime-V-rep1.36mers.unique
cd /N/dc2/projects/marinovg/2014-10-05-prokaryote-ChIP-seq/32-Francisella_tularensis_holarctica_LVS_uid58595; /N/dc2/projects/marinovg/programs/sratoolkit.2.4.0-1-ubuntu64/bin/fastq-dump.2.4.0 -Z SRR1827599 | 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/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880 -p 4 -v 2 -k 2 -m 1 -t --best --strata --sam -q --sam-nh - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Francisella_tularensis_holarctica_LVS_uid58595/bowtie-indexes/NC_007880.fa - | samtools sort - LVS_Beta_prime-V-rep2.36mers.unique