cd /N/dc2/projects/marinovg/Paramecium/RNA-seq/2015-04-13-promoters; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/Tetrahymena_thermophila.JCVI-TTA1-2.2.20.gtf Conjugation-2h-GSM692085-2x75-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/Tetrahymena_thermophila.JCVI-TTA1-2.2.20.chrom.sizes sam_reads_genes-Conjugation-2h-GSM692085-2x75 -nomulti
cd /N/dc2/projects/marinovg/Paramecium/RNA-seq/2015-04-13-promoters; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/Tetrahymena_thermophila.JCVI-TTA1-2.2.20.gtf Conjugation-8h-GSM692086-2x75-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/Tetrahymena_thermophila.JCVI-TTA1-2.2.20.chrom.sizes sam_reads_genes-Conjugation-8h-GSM692086-2x75 -nomulti
cd /N/dc2/projects/marinovg/Paramecium/RNA-seq/2015-04-13-promoters; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/Tetrahymena_thermophila.JCVI-TTA1-2.2.20.gtf Growth-m-GSM692081-2x75-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/Tetrahymena_thermophila.JCVI-TTA1-2.2.20.chrom.sizes sam_reads_genes-Growth-m-GSM692081-2x75 -nomulti
cd /N/dc2/projects/marinovg/Paramecium/RNA-seq/2015-04-13-promoters; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/Tetrahymena_thermophila.JCVI-TTA1-2.2.20.gtf Starvation-15h-VI-GSM692084-2x75-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/Tetrahymena_thermophila.JCVI-TTA1-2.2.20.chrom.sizes sam_reads_genes-Starvation-15h-VI-GSM692084-2x75 -nomulti
cd /N/dc2/projects/marinovg/Paramecium/RNA-seq/2015-04-13-promoters; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/Tetrahymena_thermophila.JCVI-TTA1-2.2.20.gtf Starvation-3h-V-GSM692083-2x75-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/Tetrahymena_thermophila.JCVI-TTA1-2.2.20.chrom.sizes sam_reads_genes-Starvation-3h-V-GSM692083-2x75 -nomulti
cd /N/dc2/projects/marinovg/Paramecium/RNA-seq/2015-04-13-promoters; python /N/dc2/projects/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/Tetrahymena_thermophila.JCVI-TTA1-2.2.20.gtf Starvation-3h-VI-GSM692082-2x75-TopHat-2.0.8-minIntron10/accepted_hits.bam /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/Tetrahymena_thermophila.JCVI-TTA1-2.2.20.chrom.sizes sam_reads_genes-Starvation-3h-VI-GSM692082-2x75 -nomulti