cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; export PATH=/N/dc2/projects/marinovg/programs/bowtie-0.12.9:/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64:$PATH; /N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 16 --no-discordant --no-mixed --microexon-search --read-realign-edit-dist 0 --library-type fr-firststrand --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --min-segment-intron 10 --min-coverage-intron 10 --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/caudatum_43c3d_annotation_v1.gtf --transcriptome-index /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/transcriptome-indexes/caudatum_43c3d_annotation_v1 -o Paramecium-caudatum-Hol_S14-2x100-TopHat-2.0.8-minIntron10 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_assembly_v1 GSF869-Doak-Ugne-Hol_S14_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-Hol_S14_R2_001.100mers.fastq.gz
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; export PATH=/N/dc2/projects/marinovg/programs/bowtie-0.12.9:/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64:$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_caudatum_43c3d/caudatum_43c3d_annotation_v1.gtf --transcriptome-index /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/transcriptome-indexes/caudatum_43c3d_annotation_v1 -o Paramecium-caudatum-no-Hol_S15-2x100-TopHat-2.0.8-minIntron10 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_assembly_v1 GSF869-Doak-Ugne-no-Hol_S15_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-no-Hol_S15_R2_001.100mers.fastq.gz