/Volumes/Bay3/Software/tophat-2.0.13.OSX_x86_64/tophat oyster.v9 /Volumes/web-1/nightingales/C_gigas/2M-HS_CCGTCC_L001_R1_001.fastq.gz
#>prep_reads:
/Volumes/Bay3/Software/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 ./tophat_out/ --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 --no-closure-search --no-coverage-search --no-microexon-search --aux-outfile=./tophat_out/prep_reads.info --index-outfile=./tophat_out/tmp/left_kept_reads.bam.index --sam-header=./tophat_out/tmp/oyster.v9_genome.bwt.samheader.sam --outfile=./tophat_out/tmp/left_kept_reads.bam /Volumes/web-1/nightingales/C_gigas/2M-HS_CCGTCC_L001_R1_001.fastq.gz
#>map_start:
/Volumes/Bay3/Software/tophat-2.0.13.OSX_x86_64/bam2fastx --all ./tophat_out/tmp/left_kept_reads.bam|/usr/local/bin/bowtie2 -k 20 -D 15 -R 2 -N 0 -L 20 -i S,1,1.25 --gbar 4 --mp 6,2 --np 1 --rdg 5,3 --rfg 5,3 --score-min C,-14,0 -p 1 --sam-no-hd -x oyster.v9 -|/Volumes/Bay3/Software/tophat-2.0.13.OSX_x86_64/fix_map_ordering --bowtie2-min-score 15 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile ./tophat_out/tmp/left_kept_reads.mapped.bam.index --sam-header ./tophat_out/tmp/oyster.v9_genome.bwt.samheader.sam - ./tophat_out/tmp/left_kept_reads.mapped.bam ./tophat_out/tmp/left_kept_reads_unmapped.bam
#>map_segments:
gzip -cd< ./tophat_out/tmp/left_kept_reads_seg1.fq.z|/usr/local/bin/bowtie2 -k 41 -N 1 -L 20 -p 1 --sam-no-hd -x oyster.v9 -|/Volumes/Bay3/Software/tophat-2.0.13.OSX_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile ./tophat_out/tmp/left_kept_reads_seg1.bam.index --sam-header ./tophat_out/tmp/oyster.v9_genome.bwt.samheader.sam - ./tophat_out/tmp/left_kept_reads_seg1.bam ./tophat_out/tmp/left_kept_reads_seg1_unmapped.bam
gzip -cd< ./tophat_out/tmp/left_kept_reads_seg2.fq.z|/usr/local/bin/bowtie2 -k 41 -N 1 -L 20 -p 1 --sam-no-hd -x oyster.v9 -|/Volumes/Bay3/Software/tophat-2.0.13.OSX_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile ./tophat_out/tmp/left_kept_reads_seg2.bam.index --sam-header ./tophat_out/tmp/oyster.v9_genome.bwt.samheader.sam - ./tophat_out/tmp/left_kept_reads_seg2.bam ./tophat_out/tmp/left_kept_reads_seg2_unmapped.bam
gzip -cd< ./tophat_out/tmp/left_kept_reads_seg3.fq.z|/usr/local/bin/bowtie2 -k 41 -N 1 -L 20 -p 1 --sam-no-hd -x oyster.v9 -|/Volumes/Bay3/Software/tophat-2.0.13.OSX_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile ./tophat_out/tmp/left_kept_reads_seg3.bam.index --sam-header ./tophat_out/tmp/oyster.v9_genome.bwt.samheader.sam - ./tophat_out/tmp/left_kept_reads_seg3.bam ./tophat_out/tmp/left_kept_reads_seg3_unmapped.bam
gzip -cd< ./tophat_out/tmp/left_kept_reads_seg4.fq.z|/usr/local/bin/bowtie2 -k 41 -N 1 -L 20 -p 1 --sam-no-hd -x oyster.v9 -|/Volumes/Bay3/Software/tophat-2.0.13.OSX_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile ./tophat_out/tmp/left_kept_reads_seg4.bam.index --sam-header ./tophat_out/tmp/oyster.v9_genome.bwt.samheader.sam - ./tophat_out/tmp/left_kept_reads_seg4.bam ./tophat_out/tmp/left_kept_reads_seg4_unmapped.bam
#>find_juncs:
/Volumes/Bay3/Software/tophat-2.0.13.OSX_x86_64/segment_juncs --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir ./tophat_out/ --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 --no-closure-search --no-coverage-search --no-microexon-search --sam-header ./tophat_out/tmp/oyster.v9_genome.bwt.samheader.sam --ium-reads ./tophat_out/tmp/left_kept_reads_seg1_unmapped.bam,./tophat_out/tmp/left_kept_reads_seg2_unmapped.bam,./tophat_out/tmp/left_kept_reads_seg3_unmapped.bam,./tophat_out/tmp/left_kept_reads_seg4_unmapped.bam oyster.v9.fa ./tophat_out/tmp/segment.juncs ./tophat_out/tmp/segment.insertions ./tophat_out/tmp/segment.deletions ./tophat_out/tmp/segment.fusions ./tophat_out/tmp/left_kept_reads.bam ./tophat_out/tmp/left_kept_reads.mapped.bam ./tophat_out/tmp/left_kept_reads_seg1.bam,./tophat_out/tmp/left_kept_reads_seg2.bam,./tophat_out/tmp/left_kept_reads_seg3.bam,./tophat_out/tmp/left_kept_reads_seg4.bam