cd /N/dc2/projects/marinovg/2016-06-14-mito-fractions; zcat GSF1106-Lynch-Marinov-Pcaudatum-2016-06-01-Fraction1_S2_R1_001.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_assembly_v1+chrM -p 16 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_assembly_v1+chrM.fa - | samtools sort -  L58-Paramecium_caudatum-fraction_1_500g.50mers.P_caudatum.unique
cd /N/dc2/projects/marinovg/2016-06-14-mito-fractions; zcat GSF1106-Lynch-Marinov-Pcaudatum-2016-06-01-Fraction2_S3_R1_001.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_assembly_v1+chrM -p 16 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_assembly_v1+chrM.fa - | samtools sort -  L59-Paramecium_caudatum-fraction_2_2000g.50mers.P_caudatum.unique
cd /N/dc2/projects/marinovg/2016-06-14-mito-fractions; zcat GSF1106-Lynch-Marinov-Pcaudatum-2016-06-01-Fraction3_S4_R1_001.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_assembly_v1+chrM -p 16 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_assembly_v1+chrM.fa - | samtools sort -  L60-Paramecium_caudatum-fraction_3_15000g.50mers.P_caudatum.unique
cd /N/dc2/projects/marinovg/2016-06-14-mito-fractions; zcat GSF1106-Lynch-Marinov-Pcaudatum-2016-06-01-Fraction1_S2_R1_001.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Enterobacter_aerogenes_KCTC_2190_uid68103/bowtie-indexes/GCA_000215745.1_ASM21574v1_genomic -p 16 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Enterobacter_aerogenes_KCTC_2190_uid68103/bowtie-indexes/GCA_000215745.1_ASM21574v1_genomic.fa - | samtools sort -  L58-Paramecium_caudatum-fraction_1_500g.50mers.Enterobacter.unique
cd /N/dc2/projects/marinovg/2016-06-14-mito-fractions; zcat GSF1106-Lynch-Marinov-Pcaudatum-2016-06-01-Fraction2_S3_R1_001.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Enterobacter_aerogenes_KCTC_2190_uid68103/bowtie-indexes/GCA_000215745.1_ASM21574v1_genomic -p 16 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Enterobacter_aerogenes_KCTC_2190_uid68103/bowtie-indexes/GCA_000215745.1_ASM21574v1_genomic.fa - | samtools sort -  L59-Paramecium_caudatum-fraction_2_2000g.50mers.Enterobacter.unique
cd /N/dc2/projects/marinovg/2016-06-14-mito-fractions; zcat GSF1106-Lynch-Marinov-Pcaudatum-2016-06-01-Fraction3_S4_R1_001.fastq.gz | python /N/dc2/projects/marinovg/code/trimfastq.py - 50 -stdout | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Enterobacter_aerogenes_KCTC_2190_uid68103/bowtie-indexes/GCA_000215745.1_ASM21574v1_genomic -p 16 -v 2 -k 2 -m 1 -t --best --strata --offrate 1 -t --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Enterobacter_aerogenes_KCTC_2190_uid68103/bowtie-indexes/GCA_000215745.1_ASM21574v1_genomic.fa - | samtools sort -  L60-Paramecium_caudatum-fraction_3_15000g.50mers.Enterobacter.unique