/usr/local2/tophat-2.0.5.Linux_x86_64/tophat --library-type fr-unstranded --min-anchor-length 8 --splice-mismatches 0 --min-intron-length 70 --max-intron-length 50000 --min-isoform-fraction 0.15 --max-multihits 20 --min-segment-intron 50 --max-segment-intron 500000 --segment-mismatches 2 --segment-length 20 --num-threads 6 --b2-sensitive -G gffread_filtered.gtf oyster.v9_90 solid0078_20091105_DH3.fastq
/usr/local2/tophat-2.0.5.Linux_x86_64/gtf_juncs gffread_filtered.gtf  > ./tophat_out/tmp/gffread_filtered.juncs
#>prep_reads:
/usr/local2/tophat-2.0.5.Linux_x86_64/prep_reads --min-anchor 8 --splice-mismatches 0 --min-report-intron 70 --max-report-intron 50000 --min-isoform-fraction 0.15 --output-dir ./tophat_out/ --max-multihits 20 --max-seg-multihits 40 --segment-length 20 --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 50000 --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 -p6 --gtf-annotations gffread_filtered.gtf --gtf-juncs ./tophat_out/tmp/gffread_filtered.juncs --no-closure-search --no-coverage-search --no-microexon-search --library-type fr-unstranded --fastq --aux-outfile=./tophat_out/prep_reads.info --index-outfile=./tophat_out/tmp/left_kept_reads.bam.index --sam-header=./tophat_out/tmp/oyster.v9_90_genome.bwt.samheader.sam --outfile=./tophat_out/tmp/left_kept_reads.bam solid0078_20091105_DH3.fastq
#>map_start:
/usr/local2/tophat-2.0.5.Linux_x86_64/gtf_to_fasta --min-anchor 8 --splice-mismatches 0 --min-report-intron 70 --max-report-intron 50000 --min-isoform-fraction 0.15 --output-dir ./tophat_out/ --max-multihits 20 --max-seg-multihits 40 --segment-length 20 --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 50000 --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 -p6 --gtf-annotations gffread_filtered.gtf --gtf-juncs ./tophat_out/tmp/gffread_filtered.juncs --no-closure-search --no-coverage-search --no-microexon-search --library-type fr-unstranded gffread_filtered.gtf oyster.v9_90.fa ./tophat_out/tmp/gffread_filtered.fa > ./tophat_out/logs/g2f.out
/usr/local2/bowtie2-2.0.0-beta7/bowtie2-build ./tophat_out/tmp/gffread_filtered.fa ./tophat_out/tmp/gffread_filtered
/usr/local2/tophat-2.0.5.Linux_x86_64/bam2fastx --all --fastq ./tophat_out/tmp/left_kept_reads.bam|/usr/local2/bowtie2-2.0.0-beta7/bowtie2-align -q -k 60 --sensitive --gbar 4 --mp 6,2 --np 1 --rdg 5,3 --rfg 5,3 --score-min C,-14,0 -p 6 --sam-no-hd -x ./tophat_out/tmp/gffread_filtered -|/usr/local2/tophat-2.0.5.Linux_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 --sam-header ./tophat_out/tmp/gffread_filtered.bwt.samheader.sam - - ./tophat_out/tmp/left_kept_reads.m2g_um.bam | /usr/local2/tophat-2.0.5.Linux_x86_64/map2gtf --sam-header ./tophat_out/tmp/oyster.v9_90_genome.bwt.samheader.sam gffread_filtered.gtf - ./tophat_out/tmp/left_kept_reads.m2g.bam > ./tophat_out/logs/m2g_left_kept_reads.out
/usr/local2/tophat-2.0.5.Linux_x86_64/bam2fastx --all --fastq ./tophat_out/tmp/left_kept_reads.m2g_um.bam|/usr/local2/bowtie2-2.0.0-beta7/bowtie2-align -q -k 20 --sensitive --gbar 4 --mp 6,2 --np 1 --rdg 5,3 --rfg 5,3 --score-min C,-14,0 -p 6 --sam-no-hd -x oyster.v9_90 -|/usr/local2/tophat-2.0.5.Linux_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.m2g_um.mapped.bam.index --sam-header ./tophat_out/tmp/oyster.v9_90_genome.bwt.samheader.sam - ./tophat_out/tmp/left_kept_reads.m2g_um.mapped.bam ./tophat_out/tmp/left_kept_reads.m2g_um_unmapped.bam
#>map_segments:
gzip -cd< ./tophat_out/tmp/left_kept_reads.m2g_um_seg1.fq.z|/usr/local2/bowtie2-2.0.0-beta7/bowtie2-align -q -k 41 -N 1 -i C,2,0 -L 20 -p 6 --sam-no-hd -x oyster.v9_90 -|/usr/local2/tophat-2.0.5.Linux_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.m2g_um_seg1.bam.index --sam-header ./tophat_out/tmp/oyster.v9_90_genome.bwt.samheader.sam - ./tophat_out/tmp/left_kept_reads.m2g_um_seg1.bam ./tophat_out/tmp/left_kept_reads.m2g_um_seg1_unmapped.bam
gzip -cd< ./tophat_out/tmp/left_kept_reads.m2g_um_seg2.fq.z|/usr/local2/bowtie2-2.0.0-beta7/bowtie2-align -q -k 41 -N 1 -i C,2,0 -L 20 -p 6 --sam-no-hd -x oyster.v9_90 -|/usr/local2/tophat-2.0.5.Linux_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.m2g_um_seg2.bam.index --sam-header ./tophat_out/tmp/oyster.v9_90_genome.bwt.samheader.sam - ./tophat_out/tmp/left_kept_reads.m2g_um_seg2.bam ./tophat_out/tmp/left_kept_reads.m2g_um_seg2_unmapped.bam
#>find_juncs:
/usr/local2/tophat-2.0.5.Linux_x86_64/segment_juncs --min-anchor 8 --splice-mismatches 0 --min-report-intron 70 --max-report-intron 50000 --min-isoform-fraction 0.15 --output-dir ./tophat_out/ --max-multihits 20 --max-seg-multihits 40 --segment-length 20 --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 50000 --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 -p6 --gtf-annotations gffread_filtered.gtf --gtf-juncs ./tophat_out/tmp/gffread_filtered.juncs --no-closure-search --no-microexon-search --library-type fr-unstranded --sam-header ./tophat_out/tmp/oyster.v9_90_genome.bwt.samheader.sam --ium-reads ./tophat_out/tmp/left_kept_reads.m2g_um_seg1_unmapped.bam,./tophat_out/tmp/left_kept_reads.m2g_um_seg2_unmapped.bam oyster.v9_90.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.m2g_um.mapped.bam ./tophat_out/tmp/left_kept_reads.m2g_um_seg1.bam,./tophat_out/tmp/left_kept_reads.m2g_um_seg2.bam
#>juncs_db:
/usr/local2/tophat-2.0.5.Linux_x86_64/juncs_db 3 31 ./tophat_out/tmp/gffread_filtered.juncs,./tophat_out/tmp/segment.juncs /dev/null /dev/null /dev/null oyster.v9_90.fa > ./tophat_out/tmp/segment_juncs.fa
/usr/local2/bowtie2-2.0.0-beta7/bowtie2-build ./tophat_out/tmp/segment_juncs.fa ./tophat_out/tmp/segment_juncs
#>map2juncs:
gzip -cd< ./tophat_out/tmp/left_kept_reads.m2g_um_seg1.fq.z|/usr/local2/bowtie2-2.0.0-beta7/bowtie2-align -q -k 41 -N 1 -i C,2,0 -L 20 -p 6 --sam-no-hd -x ./tophat_out/tmp/segment_juncs -|/usr/local2/tophat-2.0.5.Linux_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.m2g_um_seg1.to_spliced.bam.index --sam-header ./tophat_out/tmp/segment_juncs.bwt.samheader.sam - ./tophat_out/tmp/left_kept_reads.m2g_um_seg1.to_spliced.bam
gzip -cd< ./tophat_out/tmp/left_kept_reads.m2g_um_seg2.fq.z|/usr/local2/bowtie2-2.0.0-beta7/bowtie2-align -q -k 41 -N 1 -i C,2,0 -L 20 -p 6 --sam-no-hd -x ./tophat_out/tmp/segment_juncs -|/usr/local2/tophat-2.0.5.Linux_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.m2g_um_seg2.to_spliced.bam.index --sam-header ./tophat_out/tmp/segment_juncs.bwt.samheader.sam - ./tophat_out/tmp/left_kept_reads.m2g_um_seg2.to_spliced.bam
/usr/local2/tophat-2.0.5.Linux_x86_64/long_spanning_reads --min-anchor 8 --splice-mismatches 0 --min-report-intron 70 --max-report-intron 50000 --min-isoform-fraction 0.15 --output-dir ./tophat_out/ --max-multihits 20 --max-seg-multihits 40 --segment-length 20 --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 50000 --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 -p6 --gtf-annotations gffread_filtered.gtf --gtf-juncs ./tophat_out/tmp/gffread_filtered.juncs --no-closure-search --no-microexon-search --library-type fr-unstranded --sam-header ./tophat_out/tmp/oyster.v9_90_genome.bwt.samheader.sam --bowtie2-max-penalty 6 --bowtie2-min-penalty 2 --bowtie2-penalty-for-N 1 --bowtie2-read-gap-open 5 --bowtie2-read-gap-cont 3 --bowtie2-ref-gap-open 5 --bowtie2-ref-gap-cont 3 oyster.v9_90.fa ./tophat_out/tmp/left_kept_reads.m2g_um.bam ./tophat_out/tmp/gffread_filtered.juncs,./tophat_out/tmp/segment.juncs /dev/null /dev/null /dev/null ./tophat_out/tmp/left_kept_reads.m2g_um.candidates.bam ./tophat_out/tmp/left_kept_reads.m2g_um_seg1.bam,./tophat_out/tmp/left_kept_reads.m2g_um_seg2.bam ./tophat_out/tmp/left_kept_reads.m2g_um_seg1.to_spliced.bam,./tophat_out/tmp/left_kept_reads.m2g_um_seg2.to_spliced.bam
#>tophat_reports:
/usr/local2/tophat-2.0.5.Linux_x86_64/tophat_reports --min-anchor 8 --splice-mismatches 0 --min-report-intron 70 --max-report-intron 50000 --min-isoform-fraction 0.15 --output-dir ./tophat_out/ --max-multihits 20 --max-seg-multihits 40 --segment-length 20 --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 50000 --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 -p6 --gtf-annotations gffread_filtered.gtf --gtf-juncs ./tophat_out/tmp/gffread_filtered.juncs --no-closure-search --no-microexon-search --library-type fr-unstranded --sam-header ./tophat_out/tmp/oyster.v9_90_genome.bwt.samheader.sam --report-discordant-pair-alignments --report-mixed-alignments --samtools=/usr/local2/samtools-0.1.18/samtools --bowtie2-max-penalty 6 --bowtie2-min-penalty 2 --bowtie2-penalty-for-N 1 --bowtie2-read-gap-open 5 --bowtie2-read-gap-cont 3 --bowtie2-ref-gap-open 5 --bowtie2-ref-gap-cont 3 oyster.v9_90.fa ./tophat_out/junctions.bed ./tophat_out/insertions.bed ./tophat_out/deletions.bed ./tophat_out/fusions.out ./tophat_out/tmp/accepted_hits ./tophat_out/tmp/left_kept_reads.m2g.bam,./tophat_out/tmp/left_kept_reads.m2g_um.mapped.bam,./tophat_out/tmp/left_kept_reads.m2g_um.candidates ./tophat_out/tmp/left_kept_reads.bam
/usr/local2/samtools-0.1.18/samtools sort ./tophat_out/tmp/accepted_hits0.bam ./tophat_out/tmp/accepted_hits0_sorted