cd /N/dc2/projects/marinovg/Paramecium/RNA-seq/2015-04-13-promoters; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py Conjugation-2h-GSM692085_1.fastq.bz2 Conjugation-2h-GSM692085_2.fastq.bz2 | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/bowtie-indexes/Tetrahymena_thermophila.JCVI-TTA1-2.2.20.transcriptome -p 16 -e 200 -a --offrate 1 -t -X 20000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/bowtie-indexes/Tetrahymena_thermophila.JCVI-TTA1-2.2.20.transcriptome.fa - -o Conjugation-2h-GSM692085.Tetrahymena_thermophila.JCVI-TTA1-2.2.20.transcriptome.e200.bam
cd /N/dc2/projects/marinovg/Paramecium/RNA-seq/2015-04-13-promoters; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py Conjugation-8h-GSM692086_1.fastq.bz2 Conjugation-8h-GSM692086_2.fastq.bz2 | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/bowtie-indexes/Tetrahymena_thermophila.JCVI-TTA1-2.2.20.transcriptome -p 16 -e 200 -a --offrate 1 -t -X 20000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/bowtie-indexes/Tetrahymena_thermophila.JCVI-TTA1-2.2.20.transcriptome.fa - -o Conjugation-8h-GSM692086.Tetrahymena_thermophila.JCVI-TTA1-2.2.20.transcriptome.e200.bam
cd /N/dc2/projects/marinovg/Paramecium/RNA-seq/2015-04-13-promoters; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py Growth-m-GSM692081_1.fastq.bz2 Growth-m-GSM692081_2.fastq.bz2 | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/bowtie-indexes/Tetrahymena_thermophila.JCVI-TTA1-2.2.20.transcriptome -p 16 -e 200 -a --offrate 1 -t -X 20000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/bowtie-indexes/Tetrahymena_thermophila.JCVI-TTA1-2.2.20.transcriptome.fa - -o Growth-m-GSM692081.Tetrahymena_thermophila.JCVI-TTA1-2.2.20.transcriptome.e200.bam
cd /N/dc2/projects/marinovg/Paramecium/RNA-seq/2015-04-13-promoters; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py Starvation-15h-VI-GSM692084_1.fastq.bz2 Starvation-15h-VI-GSM692084_2.fastq.bz2 | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/bowtie-indexes/Tetrahymena_thermophila.JCVI-TTA1-2.2.20.transcriptome -p 16 -e 200 -a --offrate 1 -t -X 20000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/bowtie-indexes/Tetrahymena_thermophila.JCVI-TTA1-2.2.20.transcriptome.fa - -o Starvation-15h-VI-GSM692084.Tetrahymena_thermophila.JCVI-TTA1-2.2.20.transcriptome.e200.bam
cd /N/dc2/projects/marinovg/Paramecium/RNA-seq/2015-04-13-promoters; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py Starvation-3h-V-GSM692083_1.fastq.bz2 Starvation-3h-V-GSM692083_2.fastq.bz2 | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/bowtie-indexes/Tetrahymena_thermophila.JCVI-TTA1-2.2.20.transcriptome -p 16 -e 200 -a --offrate 1 -t -X 20000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/bowtie-indexes/Tetrahymena_thermophila.JCVI-TTA1-2.2.20.transcriptome.fa - -o Starvation-3h-V-GSM692083.Tetrahymena_thermophila.JCVI-TTA1-2.2.20.transcriptome.e200.bam
cd /N/dc2/projects/marinovg/Paramecium/RNA-seq/2015-04-13-promoters; python /N/dc2/projects/marinovg/code/PEFastqToTabDelimited.py Starvation-3h-VI-GSM692082_1.fastq.bz2 Starvation-3h-VI-GSM692082_2.fastq.bz2 | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/bowtie-indexes/Tetrahymena_thermophila.JCVI-TTA1-2.2.20.transcriptome -p 16 -e 200 -a --offrate 1 -t -X 20000 --sam-nh --sam --12 - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/bowtie-indexes/Tetrahymena_thermophila.JCVI-TTA1-2.2.20.transcriptome.fa - -o Starvation-3h-VI-GSM692082.Tetrahymena_thermophila.JCVI-TTA1-2.2.20.transcriptome.e200.bam