cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF869-Doak-Ugne-Hol_S14_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-Hol_S14_R2_001.100mers.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_elegans_E1-ASM64827v1/bowtie-indexes/GCA_000648275.1_ASM64827v1_genomic -p 16 -e 200 -a --offrate 1 -t -X 1000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_elegans_E1-ASM64827v1/bowtie-indexes/GCA_000648275.1_ASM64827v1_genomic.fa - -o GSF869-Doak-Ugne-Hol-Holospora_elegans_E1.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF869-Doak-Ugne-no-Hol_S15_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-no-Hol_S15_R2_001.100mers.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_elegans_E1-ASM64827v1/bowtie-indexes/GCA_000648275.1_ASM64827v1_genomic -p 16 -e 200 -a --offrate 1 -t -X 1000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_elegans_E1-ASM64827v1/bowtie-indexes/GCA_000648275.1_ASM64827v1_genomic.fa - -o GSF869-Doak-Ugne-no-Hol-Holospora_elegans_E1.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF869-Doak-Ugne-Hol_S14_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-Hol_S14_R2_001.100mers.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_obtusa_F1-ASM46966v2/bowtie-indexes/GCA_000469665.2_ASM46966v2_genomic -p 16 -e 200 -a --offrate 1 -t -X 1000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_obtusa_F1-ASM46966v2/bowtie-indexes/GCA_000469665.2_ASM46966v2_genomic.fa - -o GSF869-Doak-Ugne-Hol-Holospora_obtusa_F1.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF869-Doak-Ugne-no-Hol_S15_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-no-Hol_S15_R2_001.100mers.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_obtusa_F1-ASM46966v2/bowtie-indexes/GCA_000469665.2_ASM46966v2_genomic -p 16 -e 200 -a --offrate 1 -t -X 1000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_obtusa_F1-ASM46966v2/bowtie-indexes/GCA_000469665.2_ASM46966v2_genomic.fa - -o GSF869-Doak-Ugne-no-Hol-Holospora_obtusa_F1.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF869-Doak-Ugne-Hol_S14_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-Hol_S14_R2_001.100mers.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_undulata_HU1-ASM38817v3/bowtie-indexes/GCA_000388175.3_ASM38817v3_genomic -p 16 -e 200 -a --offrate 1 -t -X 1000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_undulata_HU1-ASM38817v3/bowtie-indexes/GCA_000388175.3_ASM38817v3_genomic.fa - -o GSF869-Doak-Ugne-Hol-Holospora_undulata_HU1.bam
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py GSF869-Doak-Ugne-no-Hol_S15_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-no-Hol_S15_R2_001.100mers.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_undulata_HU1-ASM38817v3/bowtie-indexes/GCA_000388175.3_ASM38817v3_genomic -p 16 -e 200 -a --offrate 1 -t -X 1000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_undulata_HU1-ASM38817v3/bowtie-indexes/GCA_000388175.3_ASM38817v3_genomic.fa - -o GSF869-Doak-Ugne-no-HolHolospora_undulata_HU1.bam