cd /N/dc2/projects/marinovg/2015-05-27-data; 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/Paramecium_primaurelia_Ir4-2/primaurelia_Ir4-2_annotation_v1.gtf --transcriptome-index /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/transcriptome-indexes/primaurelia_Ir4-2_annotation_v1 -o Paramecium-caudatum-A39-2x100-TopHat-2.0.8-minIntron10 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1 Sample_A39-TomD_LynchAB_RP4.100mers.read1.fastq.gz Sample_A39-TomD_LynchAB_RP4.100mers.read2.fastq.gz