cd /N/dc2/projects/marinovg/Paramecium/RNA-seq/2015-04-13-promoters; export PATH=/N/dc2/projects/marinovg/programs/bowtie-0.12.9:/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64:$PATH; /N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 16 --no-discordant --no-mixed --microexon-search --read-realign-edit-dist 0 --library-type fr-firststrand --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --min-segment-intron 10 --min-coverage-intron 10 --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/Tetrahymena_thermophila.JCVI-TTA1-2.2.20.gtf --transcriptome-index /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/transcriptome-indexes/Tetrahymena_thermophila.JCVI-TTA1-2.2.20 -o Conjugation-2h-GSM692085-2x75-TopHat-2.0.8-minIntron10 /N/dc2/projects/marinovg/genomes/Ciliates/Tetrahymena_thermophila/bowtie-indexes/Tetrahymena_thermophila.JCVI-TTA1-2.2.20 Conjugation-2h-GSM692085_1.fastq.bz2 Conjugation-2h-GSM692085_2.fastq.bz2