cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py PbU4-1_CGGCTATG-TAATCTTA_L001_R1_001.100mers.fastq.gz PbU4-1_CGGCTATG-TAATCTTA_L001_R2_001.100mers.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT biaurelia_V1-4_assembly_v1.fa - | samtools sort - PbU4-1_CGGCTATG-TAATCTTA_L001_R1_001.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py 100709_IRIS_0005-s_7_1_sequence.100mers.fastq.gz 100709_IRIS_0005-s_7_2_sequence.100mers.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT biaurelia_V1-4_assembly_v1.fa - | samtools sort - 100709_IRIS_0005-s_7_1_sequence.2x100mers.unique
cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py 100727_IRIS_0006-pbia_1_sequence.100mers.fastq.gz 100727_IRIS_0006-pbia_2_sequence.100mers.fastq.gz | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 -p 16 -e 200 -k 2 -m 1 -t --best --strata --offrate 1 -t -X 2000 --sam-nh --sam --12 - | samtools view -bT biaurelia_V1-4_assembly_v1.fa - | samtools sort - 100727_IRIS_0006-pbia_1_sequence.2x100mers.unique