/software/bi/bin/tophat -o A8DE_13066_ATTCCT -p 8 -r 180 --mate-std-dev 80 --library-type fr-firststrand -G ../anno/genes.gtf ../anno/genome ../../data/2016-03-02/A8DE_13066_ATTCCT_read1.fastq.gz ../../data/2016-03-02/A8DE_13066_ATTCCT_read2.fastq.gz
/nfs/software/bi/el6.3/version/tophat/tophat-2.0.14.Linux_x86_64/gtf_juncs ../anno/genes.gtf  > A8DE_13066_ATTCCT/tmp/genes.juncs
#>prep_reads:
/nfs/software/bi/el6.3/version/tophat/tophat-2.0.14.Linux_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 A8DE_13066_ATTCCT/ --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 --inner-dist-mean 180 --inner-dist-std-dev 80 --gtf-annotations ../anno/genes.gtf --gtf-juncs A8DE_13066_ATTCCT/tmp/genes.juncs --no-closure-search --no-coverage-search --no-microexon-search --library-type fr-firststrand --aux-outfile=A8DE_13066_ATTCCT/prep_reads.info --index-outfile=A8DE_13066_ATTCCT/tmp/%side%_kept_reads.bam.index --sam-header=A8DE_13066_ATTCCT/tmp/genome_genome.bwt.samheader.sam --outfile=A8DE_13066_ATTCCT/tmp/%side%_kept_reads.bam ../../data/2016-03-02/A8DE_13066_ATTCCT_read1.fastq.gz ../../data/2016-03-02/A8DE_13066_ATTCCT_read2.fastq.gz
#>map_start:
/nfs/software/bi/el6.3/version/tophat/tophat-2.0.14.Linux_x86_64/gtf_to_fasta --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir A8DE_13066_ATTCCT/ --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 --inner-dist-mean 180 --inner-dist-std-dev 80 --gtf-annotations ../anno/genes.gtf --gtf-juncs A8DE_13066_ATTCCT/tmp/genes.juncs --no-closure-search --no-coverage-search --no-microexon-search --library-type fr-firststrand ../anno/genes.gtf ../anno/genome.fa A8DE_13066_ATTCCT/tmp/genes.fa > A8DE_13066_ATTCCT/logs/g2f.out
/software/bi/bin/bowtie2-build A8DE_13066_ATTCCT/tmp/genes.fa A8DE_13066_ATTCCT/tmp/genes
/nfs/software/bi/el6.3/version/tophat/tophat-2.0.14.Linux_x86_64/bam2fastx --all A8DE_13066_ATTCCT/tmp/left_kept_reads.bam|/software/bi/bin/bowtie2 -k 60 -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 8 --sam-no-hd -x A8DE_13066_ATTCCT/tmp/genes -|/nfs/software/bi/el6.3/version/tophat/tophat-2.0.14.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 A8DE_13066_ATTCCT/tmp/genes.bwt.samheader.sam - - A8DE_13066_ATTCCT/tmp/left_kept_reads.m2g_um.bam | /nfs/software/bi/el6.3/version/tophat/tophat-2.0.14.Linux_x86_64/map2gtf --sam-header A8DE_13066_ATTCCT/tmp/genome_genome.bwt.samheader.sam A8DE_13066_ATTCCT/tmp/genes.fa.tlst - A8DE_13066_ATTCCT/tmp/left_kept_reads.m2g.bam > A8DE_13066_ATTCCT/logs/m2g_left_kept_reads.out
/nfs/software/bi/el6.3/version/tophat/tophat-2.0.14.Linux_x86_64/bam2fastx --all A8DE_13066_ATTCCT/tmp/right_kept_reads.bam|/software/bi/bin/bowtie2 -k 60 -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 8 --sam-no-hd -x A8DE_13066_ATTCCT/tmp/genes -|/nfs/software/bi/el6.3/version/tophat/tophat-2.0.14.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 A8DE_13066_ATTCCT/tmp/genes.bwt.samheader.sam - - A8DE_13066_ATTCCT/tmp/right_kept_reads.m2g_um.bam | /nfs/software/bi/el6.3/version/tophat/tophat-2.0.14.Linux_x86_64/map2gtf --sam-header A8DE_13066_ATTCCT/tmp/genome_genome.bwt.samheader.sam A8DE_13066_ATTCCT/tmp/genes.fa.tlst - A8DE_13066_ATTCCT/tmp/right_kept_reads.m2g.bam > A8DE_13066_ATTCCT/logs/m2g_right_kept_reads.out
/nfs/software/bi/el6.3/version/tophat/tophat-2.0.14.Linux_x86_64/bam2fastx --all A8DE_13066_ATTCCT/tmp/left_kept_reads.m2g_um.bam|/software/bi/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 8 --sam-no-hd -x ../anno/genome -|/nfs/software/bi/el6.3/version/tophat/tophat-2.0.14.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 A8DE_13066_ATTCCT/tmp/left_kept_reads.m2g_um.mapped.bam.index --sam-header A8DE_13066_ATTCCT/tmp/genome_genome.bwt.samheader.sam - A8DE_13066_ATTCCT/tmp/left_kept_reads.m2g_um.mapped.bam A8DE_13066_ATTCCT/tmp/left_kept_reads.m2g_um_unmapped.bam
#>map_segments:
gzip -cd< A8DE_13066_ATTCCT/tmp/left_kept_reads.m2g_um_seg1.fq.z|/software/bi/bin/bowtie2 -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x ../anno/genome -|/nfs/software/bi/el6.3/version/tophat/tophat-2.0.14.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 A8DE_13066_ATTCCT/tmp/left_kept_reads.m2g_um_seg1.bam.index --sam-header A8DE_13066_ATTCCT/tmp/genome_genome.bwt.samheader.sam - A8DE_13066_ATTCCT/tmp/left_kept_reads.m2g_um_seg1.bam A8DE_13066_ATTCCT/tmp/left_kept_reads.m2g_um_seg1_unmapped.bam
gzip -cd< A8DE_13066_ATTCCT/tmp/left_kept_reads.m2g_um_seg2.fq.z|/software/bi/bin/bowtie2 -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x ../anno/genome -|/nfs/software/bi/el6.3/version/tophat/tophat-2.0.14.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 A8DE_13066_ATTCCT/tmp/left_kept_reads.m2g_um_seg2.bam.index --sam-header A8DE_13066_ATTCCT/tmp/genome_genome.bwt.samheader.sam - A8DE_13066_ATTCCT/tmp/left_kept_reads.m2g_um_seg2.bam A8DE_13066_ATTCCT/tmp/left_kept_reads.m2g_um_seg2_unmapped.bam
/nfs/software/bi/el6.3/version/tophat/tophat-2.0.14.Linux_x86_64/bam2fastx --all A8DE_13066_ATTCCT/tmp/right_kept_reads.m2g_um.bam|/software/bi/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 8 --sam-no-hd -x ../anno/genome -|/nfs/software/bi/el6.3/version/tophat/tophat-2.0.14.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 A8DE_13066_ATTCCT/tmp/right_kept_reads.m2g_um.mapped.bam.index --sam-header A8DE_13066_ATTCCT/tmp/genome_genome.bwt.samheader.sam - A8DE_13066_ATTCCT/tmp/right_kept_reads.m2g_um.mapped.bam A8DE_13066_ATTCCT/tmp/right_kept_reads.m2g_um_unmapped.bam
#>map_segments:
gzip -cd< A8DE_13066_ATTCCT/tmp/right_kept_reads.m2g_um_seg1.fq.z|/software/bi/bin/bowtie2 -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x ../anno/genome -|/nfs/software/bi/el6.3/version/tophat/tophat-2.0.14.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 A8DE_13066_ATTCCT/tmp/right_kept_reads.m2g_um_seg1.bam.index --sam-header A8DE_13066_ATTCCT/tmp/genome_genome.bwt.samheader.sam - A8DE_13066_ATTCCT/tmp/right_kept_reads.m2g_um_seg1.bam A8DE_13066_ATTCCT/tmp/right_kept_reads.m2g_um_seg1_unmapped.bam
gzip -cd< A8DE_13066_ATTCCT/tmp/right_kept_reads.m2g_um_seg2.fq.z|/software/bi/bin/bowtie2 -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x ../anno/genome -|/nfs/software/bi/el6.3/version/tophat/tophat-2.0.14.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 A8DE_13066_ATTCCT/tmp/right_kept_reads.m2g_um_seg2.bam.index --sam-header A8DE_13066_ATTCCT/tmp/genome_genome.bwt.samheader.sam - A8DE_13066_ATTCCT/tmp/right_kept_reads.m2g_um_seg2.bam A8DE_13066_ATTCCT/tmp/right_kept_reads.m2g_um_seg2_unmapped.bam
#>find_juncs:
/nfs/software/bi/el6.3/version/tophat/tophat-2.0.14.Linux_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 A8DE_13066_ATTCCT/ --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 --inner-dist-mean 180 --inner-dist-std-dev 80 --gtf-annotations ../anno/genes.gtf --gtf-juncs A8DE_13066_ATTCCT/tmp/genes.juncs --no-closure-search --no-microexon-search --library-type fr-firststrand --sam-header A8DE_13066_ATTCCT/tmp/genome_genome.bwt.samheader.sam --ium-reads A8DE_13066_ATTCCT/tmp/left_kept_reads.m2g_um_seg1_unmapped.bam,A8DE_13066_ATTCCT/tmp/left_kept_reads.m2g_um_seg2_unmapped.bam,A8DE_13066_ATTCCT/tmp/right_kept_reads.m2g_um_seg1_unmapped.bam,A8DE_13066_ATTCCT/tmp/right_kept_reads.m2g_um_seg2_unmapped.bam ../anno/genome.fa A8DE_13066_ATTCCT/tmp/segment.juncs A8DE_13066_ATTCCT/tmp/segment.insertions A8DE_13066_ATTCCT/tmp/segment.deletions A8DE_13066_ATTCCT/tmp/segment.fusions A8DE_13066_ATTCCT/tmp/left_kept_reads.bam A8DE_13066_ATTCCT/tmp/left_kept_reads.m2g_um.mapped.bam A8DE_13066_ATTCCT/tmp/left_kept_reads.m2g_um_seg1.bam,A8DE_13066_ATTCCT/tmp/left_kept_reads.m2g_um_seg2.bam A8DE_13066_ATTCCT/tmp/right_kept_reads.bam A8DE_13066_ATTCCT/tmp/right_kept_reads.m2g_um.mapped.bam A8DE_13066_ATTCCT/tmp/right_kept_reads.m2g_um_seg1.bam,A8DE_13066_ATTCCT/tmp/right_kept_reads.m2g_um_seg2.bam
#>juncs_db:
/nfs/software/bi/el6.3/version/tophat/tophat-2.0.14.Linux_x86_64/juncs_db 3 25 A8DE_13066_ATTCCT/tmp/genes.juncs,A8DE_13066_ATTCCT/tmp/segment.juncs /dev/null /dev/null /dev/null ../anno/genome.fa > A8DE_13066_ATTCCT/tmp/segment_juncs.fa
/software/bi/bin/bowtie2-build A8DE_13066_ATTCCT/tmp/segment_juncs.fa A8DE_13066_ATTCCT/tmp/segment_juncs
#>map2juncs:
gzip -cd< A8DE_13066_ATTCCT/tmp/left_kept_reads.m2g_um_seg1.fq.z|/software/bi/bin/bowtie2 -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x A8DE_13066_ATTCCT/tmp/segment_juncs -|/nfs/software/bi/el6.3/version/tophat/tophat-2.0.14.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 A8DE_13066_ATTCCT/tmp/left_kept_reads.m2g_um_seg1.to_spliced.bam.index --sam-header A8DE_13066_ATTCCT/tmp/segment_juncs.bwt.samheader.sam - A8DE_13066_ATTCCT/tmp/left_kept_reads.m2g_um_seg1.to_spliced.bam
gzip -cd< A8DE_13066_ATTCCT/tmp/left_kept_reads.m2g_um_seg2.fq.z|/software/bi/bin/bowtie2 -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x A8DE_13066_ATTCCT/tmp/segment_juncs -|/nfs/software/bi/el6.3/version/tophat/tophat-2.0.14.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 A8DE_13066_ATTCCT/tmp/left_kept_reads.m2g_um_seg2.to_spliced.bam.index --sam-header A8DE_13066_ATTCCT/tmp/segment_juncs.bwt.samheader.sam - A8DE_13066_ATTCCT/tmp/left_kept_reads.m2g_um_seg2.to_spliced.bam
/nfs/software/bi/el6.3/version/tophat/tophat-2.0.14.Linux_x86_64/long_spanning_reads --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir A8DE_13066_ATTCCT/ --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 --inner-dist-mean 180 --inner-dist-std-dev 80 --gtf-annotations ../anno/genes.gtf --gtf-juncs A8DE_13066_ATTCCT/tmp/genes.juncs --no-closure-search --no-microexon-search --library-type fr-firststrand --sam-header A8DE_13066_ATTCCT/tmp/genome_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 ../anno/genome.fa A8DE_13066_ATTCCT/tmp/left_kept_reads.m2g_um.bam A8DE_13066_ATTCCT/tmp/genes.juncs,A8DE_13066_ATTCCT/tmp/segment.juncs /dev/null /dev/null /dev/null A8DE_13066_ATTCCT/tmp/left_kept_reads.m2g_um.candidates.bam A8DE_13066_ATTCCT/tmp/left_kept_reads.m2g_um_seg1.bam,A8DE_13066_ATTCCT/tmp/left_kept_reads.m2g_um_seg2.bam A8DE_13066_ATTCCT/tmp/left_kept_reads.m2g_um_seg1.to_spliced.bam,A8DE_13066_ATTCCT/tmp/left_kept_reads.m2g_um_seg2.to_spliced.bam
gzip -cd< A8DE_13066_ATTCCT/tmp/right_kept_reads.m2g_um_seg1.fq.z|/software/bi/bin/bowtie2 -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x A8DE_13066_ATTCCT/tmp/segment_juncs -|/nfs/software/bi/el6.3/version/tophat/tophat-2.0.14.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 A8DE_13066_ATTCCT/tmp/right_kept_reads.m2g_um_seg1.to_spliced.bam.index --sam-header A8DE_13066_ATTCCT/tmp/segment_juncs.bwt.samheader.sam - A8DE_13066_ATTCCT/tmp/right_kept_reads.m2g_um_seg1.to_spliced.bam
gzip -cd< A8DE_13066_ATTCCT/tmp/right_kept_reads.m2g_um_seg2.fq.z|/software/bi/bin/bowtie2 -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x A8DE_13066_ATTCCT/tmp/segment_juncs -|/nfs/software/bi/el6.3/version/tophat/tophat-2.0.14.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 A8DE_13066_ATTCCT/tmp/right_kept_reads.m2g_um_seg2.to_spliced.bam.index --sam-header A8DE_13066_ATTCCT/tmp/segment_juncs.bwt.samheader.sam - A8DE_13066_ATTCCT/tmp/right_kept_reads.m2g_um_seg2.to_spliced.bam
/nfs/software/bi/el6.3/version/tophat/tophat-2.0.14.Linux_x86_64/long_spanning_reads --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir A8DE_13066_ATTCCT/ --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 --inner-dist-mean 180 --inner-dist-std-dev 80 --gtf-annotations ../anno/genes.gtf --gtf-juncs A8DE_13066_ATTCCT/tmp/genes.juncs --no-closure-search --no-microexon-search --library-type fr-firststrand --sam-header A8DE_13066_ATTCCT/tmp/genome_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 ../anno/genome.fa A8DE_13066_ATTCCT/tmp/right_kept_reads.m2g_um.bam A8DE_13066_ATTCCT/tmp/genes.juncs,A8DE_13066_ATTCCT/tmp/segment.juncs /dev/null /dev/null /dev/null A8DE_13066_ATTCCT/tmp/right_kept_reads.m2g_um.candidates.bam A8DE_13066_ATTCCT/tmp/right_kept_reads.m2g_um_seg1.bam,A8DE_13066_ATTCCT/tmp/right_kept_reads.m2g_um_seg2.bam A8DE_13066_ATTCCT/tmp/right_kept_reads.m2g_um_seg1.to_spliced.bam,A8DE_13066_ATTCCT/tmp/right_kept_reads.m2g_um_seg2.to_spliced.bam
#>tophat_reports:
/nfs/software/bi/el6.3/version/tophat/tophat-2.0.14.Linux_x86_64/tophat_reports --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir A8DE_13066_ATTCCT/ --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 --inner-dist-mean 180 --inner-dist-std-dev 80 --gtf-annotations ../anno/genes.gtf --gtf-juncs A8DE_13066_ATTCCT/tmp/genes.juncs --no-closure-search --no-microexon-search --library-type fr-firststrand --sam-header A8DE_13066_ATTCCT/tmp/genome_genome.bwt.samheader.sam --report-discordant-pair-alignments --report-mixed-alignments --samtools=/nfs/software/bi/el6.3/version/tophat/tophat-2.0.14.Linux_x86_64/samtools_0.1.18 --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 ../anno/genome.fa A8DE_13066_ATTCCT/junctions.bed A8DE_13066_ATTCCT/insertions.bed A8DE_13066_ATTCCT/deletions.bed A8DE_13066_ATTCCT/fusions.out A8DE_13066_ATTCCT/tmp/accepted_hits A8DE_13066_ATTCCT/tmp/left_kept_reads.m2g.bam,A8DE_13066_ATTCCT/tmp/left_kept_reads.m2g_um.mapped.bam,A8DE_13066_ATTCCT/tmp/left_kept_reads.m2g_um.candidates A8DE_13066_ATTCCT/tmp/left_kept_reads.bam A8DE_13066_ATTCCT/tmp/right_kept_reads.m2g.bam,A8DE_13066_ATTCCT/tmp/right_kept_reads.m2g_um.mapped.bam,A8DE_13066_ATTCCT/tmp/right_kept_reads.m2g_um.candidates A8DE_13066_ATTCCT/tmp/right_kept_reads.bam
/nfs/software/bi/el6.3/version/tophat/tophat-2.0.14.Linux_x86_64/samtools_0.1.18 sort A8DE_13066_ATTCCT/tmp/accepted_hits0.bam A8DE_13066_ATTCCT/tmp/accepted_hits0_sorted
/nfs/software/bi/el6.3/version/tophat/tophat-2.0.14.Linux_x86_64/samtools_0.1.18 sort A8DE_13066_ATTCCT/tmp/accepted_hits1.bam A8DE_13066_ATTCCT/tmp/accepted_hits1_sorted
/nfs/software/bi/el6.3/version/tophat/tophat-2.0.14.Linux_x86_64/samtools_0.1.18 sort A8DE_13066_ATTCCT/tmp/accepted_hits2.bam A8DE_13066_ATTCCT/tmp/accepted_hits2_sorted
/nfs/software/bi/el6.3/version/tophat/tophat-2.0.14.Linux_x86_64/samtools_0.1.18 sort A8DE_13066_ATTCCT/tmp/accepted_hits3.bam A8DE_13066_ATTCCT/tmp/accepted_hits3_sorted
/nfs/software/bi/el6.3/version/tophat/tophat-2.0.14.Linux_x86_64/samtools_0.1.18 sort A8DE_13066_ATTCCT/tmp/accepted_hits4.bam A8DE_13066_ATTCCT/tmp/accepted_hits4_sorted
/nfs/software/bi/el6.3/version/tophat/tophat-2.0.14.Linux_x86_64/samtools_0.1.18 sort A8DE_13066_ATTCCT/tmp/accepted_hits5.bam A8DE_13066_ATTCCT/tmp/accepted_hits5_sorted
/nfs/software/bi/el6.3/version/tophat/tophat-2.0.14.Linux_x86_64/samtools_0.1.18 sort A8DE_13066_ATTCCT/tmp/accepted_hits6.bam A8DE_13066_ATTCCT/tmp/accepted_hits6_sorted
/nfs/software/bi/el6.3/version/tophat/tophat-2.0.14.Linux_x86_64/samtools_0.1.18 sort A8DE_13066_ATTCCT/tmp/accepted_hits7.bam A8DE_13066_ATTCCT/tmp/accepted_hits7_sorted
/nfs/software/bi/el6.3/version/tophat/tophat-2.0.14.Linux_x86_64/samtools_0.1.18 merge -f -h A8DE_13066_ATTCCT/tmp/genome_genome.bwt.samheader.sam A8DE_13066_ATTCCT/accepted_hits.bam A8DE_13066_ATTCCT/tmp/accepted_hits0_sorted.bam A8DE_13066_ATTCCT/tmp/accepted_hits1_sorted.bam A8DE_13066_ATTCCT/tmp/accepted_hits2_sorted.bam A8DE_13066_ATTCCT/tmp/accepted_hits3_sorted.bam A8DE_13066_ATTCCT/tmp/accepted_hits4_sorted.bam A8DE_13066_ATTCCT/tmp/accepted_hits5_sorted.bam A8DE_13066_ATTCCT/tmp/accepted_hits6_sorted.bam A8DE_13066_ATTCCT/tmp/accepted_hits7_sorted.bam
/nfs/software/bi/el6.3/version/tophat/tophat-2.0.14.Linux_x86_64/bam_merge -Q --sam-header A8DE_13066_ATTCCT/tmp/genome_genome.bwt.samheader.sam A8DE_13066_ATTCCT/unmapped.bam A8DE_13066_ATTCCT/tmp/unmapped_left_0.bam A8DE_13066_ATTCCT/tmp/unmapped_right_0.bam A8DE_13066_ATTCCT/tmp/unmapped_left_1.bam A8DE_13066_ATTCCT/tmp/unmapped_right_1.bam A8DE_13066_ATTCCT/tmp/unmapped_left_2.bam A8DE_13066_ATTCCT/tmp/unmapped_right_2.bam A8DE_13066_ATTCCT/tmp/unmapped_left_3.bam A8DE_13066_ATTCCT/tmp/unmapped_right_3.bam A8DE_13066_ATTCCT/tmp/unmapped_left_4.bam A8DE_13066_ATTCCT/tmp/unmapped_right_4.bam A8DE_13066_ATTCCT/tmp/unmapped_left_5.bam A8DE_13066_ATTCCT/tmp/unmapped_right_5.bam A8DE_13066_ATTCCT/tmp/unmapped_left_6.bam A8DE_13066_ATTCCT/tmp/unmapped_right_6.bam A8DE_13066_ATTCCT/tmp/unmapped_left_7.bam A8DE_13066_ATTCCT/tmp/unmapped_right_7.bam
#>alldone: