cd /N/dc2/projects/marinovg/2015-05-06-data; export PATH=/N/dc2/projects/marinovg/programs/bowtie-0.12.9:/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64:$PATH; /N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 16 --no-discordant --no-mixed --microexon-search --read-realign-edit-dist 0 --library-type fr-firststrand --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --min-segment-intron 10 --min-coverage-intron 10 -o Paramecium_octaurelia_K8_CA1-Sample_8V-2x100-TopHat-2.0.8-minIntron10  /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf  /N/dc2/projects/marinovg/2015-05-06-data/Sample_8V.end1.100mers.fastq.bz2 /N/dc2/projects/marinovg/2015-05-06-data/Sample_8V.end2.100mers.fastq.bz2
cd /N/dc2/projects/marinovg/2015-05-06-data; export PATH=/N/dc2/projects/marinovg/programs/bowtie-0.12.9:/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64:$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 -o Paramecium_octaurelia_K8_CA1-Sample_8D1-2x100-TopHat-2.0.8-minIntron10  /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_octaurelia_K8_CA1/bowtie-indexes/Octaurelia_K8_CA1.scf  /N/dc2/projects/marinovg/2015-05-06-data/Sample_8D1.end1.100mers.fastq.bz2 /N/dc2/projects/marinovg/2015-05-06-data/Sample_8D1.end2.100mers.fastq.bz2
cd /N/dc2/projects/marinovg/2015-05-06-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 -o Paramecium_tredecaurelia_209_CA2-Sample_209_13-2x100-TopHat-2.0.8-minIntron10  /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tredecaurelia_209_CA2/bowtie-indexes/tredecaurelia_209_CA2.scf /N/dc2/projects/marinovg/2015-05-06-data/Sample_209_13.end1.100mers.fastq.bz2 /N/dc2/projects/marinovg/2015-05-06-data/Sample_209_13.end2.100mers.fastq.bz2