/usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64/tophat -p 8 -o /Volumes/web/halfshell/qdod3/ /Volumes/web/halfshell/qdod3/Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel /Volumes/web/nightingales/C_gigas/2M_AGTCAA_L001_R1_001.fastq.gz
#>prep_reads:
/usr/local/bioinformatics/tophat-2.0.13.OSX_x86_64/prep_reads --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir /Volumes/web/halfshell/qdod3// --max-multihits 20 --max-seg-multihits 40 --segment-length 25 --segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 --min-coverage-intron 50 --max-coverage-intron 20000 --min-segment-intron 50 --max-segment-intron 500000 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --max-insertion-length 3 --max-deletion-length 3 -z gzip -p8 --no-closure-search --no-coverage-search --no-microexon-search --aux-outfile=/Volumes/web/halfshell/qdod3//prep_reads.info --index-outfile=/Volumes/web/halfshell/qdod3//tmp/left_kept_reads.bam.index --sam-header=/Volumes/web/halfshell/qdod3//tmp/Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel_genome.bwt.samheader.sam --outfile=/Volumes/web/halfshell/qdod3//tmp/left_kept_reads.bam /Volumes/web/nightingales/C_gigas/2M_AGTCAA_L001_R1_001.fastq.gz