/share/pkg.7/tophat/2.1.1/install/bin/tophat --num-threads 4 --no-coverage-search -o ../out/tophat_pe_qsub ../ref/test_ref ../data/reads_1.fq ../data/reads_2.fq
#>prep_reads:
/share/pkg.7/tophat/2.1.1/install/bin/prep_reads --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir ../out/tophat_pe_qsub/ --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 -p4 --inner-dist-mean 50 --inner-dist-std-dev 20 --no-closure-search --no-coverage-search --no-microexon-search --aux-outfile=../out/tophat_pe_qsub/prep_reads.info --index-outfile=../out/tophat_pe_qsub/tmp/%side%_kept_reads.bam.index --sam-header=../out/tophat_pe_qsub/tmp/test_ref_genome.bwt.samheader.sam --outfile=../out/tophat_pe_qsub/tmp/%side%_kept_reads.bam ../data/reads_1.fq ../data/reads_2.fq
#>map_start:
/share/pkg.7/tophat/2.1.1/install/bin/bam2fastx --all ../out/tophat_pe_qsub/tmp/left_kept_reads.bam|/share/pkg.7/bowtie2/2.4.2/install/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 4 --sam-no-hd -x ../ref/test_ref -|/share/pkg.7/tophat/2.1.1/install/bin/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 ../out/tophat_pe_qsub/tmp/left_kept_reads.mapped.bam.index --sam-header ../out/tophat_pe_qsub/tmp/test_ref_genome.bwt.samheader.sam - ../out/tophat_pe_qsub/tmp/left_kept_reads.mapped.bam ../out/tophat_pe_qsub/tmp/left_kept_reads_unmapped.bam
#>map_segments:
gzip -cd< ../out/tophat_pe_qsub/tmp/left_kept_reads_seg1.fq.z|/share/pkg.7/bowtie2/2.4.2/install/bin/bowtie2 -k 41 -N 1 -L 20 -p 4 --sam-no-hd -x ../ref/test_ref -|/share/pkg.7/tophat/2.1.1/install/bin/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 ../out/tophat_pe_qsub/tmp/left_kept_reads_seg1.bam.index --sam-header ../out/tophat_pe_qsub/tmp/test_ref_genome.bwt.samheader.sam - ../out/tophat_pe_qsub/tmp/left_kept_reads_seg1.bam ../out/tophat_pe_qsub/tmp/left_kept_reads_seg1_unmapped.bam
gzip -cd< ../out/tophat_pe_qsub/tmp/left_kept_reads_seg2.fq.z|/share/pkg.7/bowtie2/2.4.2/install/bin/bowtie2 -k 41 -N 1 -L 20 -p 4 --sam-no-hd -x ../ref/test_ref -|/share/pkg.7/tophat/2.1.1/install/bin/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 ../out/tophat_pe_qsub/tmp/left_kept_reads_seg2.bam.index --sam-header ../out/tophat_pe_qsub/tmp/test_ref_genome.bwt.samheader.sam - ../out/tophat_pe_qsub/tmp/left_kept_reads_seg2.bam ../out/tophat_pe_qsub/tmp/left_kept_reads_seg2_unmapped.bam
gzip -cd< ../out/tophat_pe_qsub/tmp/left_kept_reads_seg3.fq.z|/share/pkg.7/bowtie2/2.4.2/install/bin/bowtie2 -k 41 -N 1 -L 20 -p 4 --sam-no-hd -x ../ref/test_ref -|/share/pkg.7/tophat/2.1.1/install/bin/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 ../out/tophat_pe_qsub/tmp/left_kept_reads_seg3.bam.index --sam-header ../out/tophat_pe_qsub/tmp/test_ref_genome.bwt.samheader.sam - ../out/tophat_pe_qsub/tmp/left_kept_reads_seg3.bam ../out/tophat_pe_qsub/tmp/left_kept_reads_seg3_unmapped.bam
/share/pkg.7/tophat/2.1.1/install/bin/bam2fastx --all ../out/tophat_pe_qsub/tmp/right_kept_reads.bam|/share/pkg.7/bowtie2/2.4.2/install/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 4 --sam-no-hd -x ../ref/test_ref -|/share/pkg.7/tophat/2.1.1/install/bin/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 ../out/tophat_pe_qsub/tmp/right_kept_reads.mapped.bam.index --sam-header ../out/tophat_pe_qsub/tmp/test_ref_genome.bwt.samheader.sam - ../out/tophat_pe_qsub/tmp/right_kept_reads.mapped.bam ../out/tophat_pe_qsub/tmp/right_kept_reads_unmapped.bam
#>map_segments:
gzip -cd< ../out/tophat_pe_qsub/tmp/right_kept_reads_seg1.fq.z|/share/pkg.7/bowtie2/2.4.2/install/bin/bowtie2 -k 41 -N 1 -L 20 -p 4 --sam-no-hd -x ../ref/test_ref -|/share/pkg.7/tophat/2.1.1/install/bin/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 ../out/tophat_pe_qsub/tmp/right_kept_reads_seg1.bam.index --sam-header ../out/tophat_pe_qsub/tmp/test_ref_genome.bwt.samheader.sam - ../out/tophat_pe_qsub/tmp/right_kept_reads_seg1.bam ../out/tophat_pe_qsub/tmp/right_kept_reads_seg1_unmapped.bam
gzip -cd< ../out/tophat_pe_qsub/tmp/right_kept_reads_seg2.fq.z|/share/pkg.7/bowtie2/2.4.2/install/bin/bowtie2 -k 41 -N 1 -L 20 -p 4 --sam-no-hd -x ../ref/test_ref -|/share/pkg.7/tophat/2.1.1/install/bin/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 ../out/tophat_pe_qsub/tmp/right_kept_reads_seg2.bam.index --sam-header ../out/tophat_pe_qsub/tmp/test_ref_genome.bwt.samheader.sam - ../out/tophat_pe_qsub/tmp/right_kept_reads_seg2.bam ../out/tophat_pe_qsub/tmp/right_kept_reads_seg2_unmapped.bam
gzip -cd< ../out/tophat_pe_qsub/tmp/right_kept_reads_seg3.fq.z|/share/pkg.7/bowtie2/2.4.2/install/bin/bowtie2 -k 41 -N 1 -L 20 -p 4 --sam-no-hd -x ../ref/test_ref -|/share/pkg.7/tophat/2.1.1/install/bin/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 ../out/tophat_pe_qsub/tmp/right_kept_reads_seg3.bam.index --sam-header ../out/tophat_pe_qsub/tmp/test_ref_genome.bwt.samheader.sam - ../out/tophat_pe_qsub/tmp/right_kept_reads_seg3.bam ../out/tophat_pe_qsub/tmp/right_kept_reads_seg3_unmapped.bam
#>find_juncs:
/share/pkg.7/tophat/2.1.1/install/bin/segment_juncs --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir ../out/tophat_pe_qsub/ --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 -p4 --inner-dist-mean 50 --inner-dist-std-dev 20 --no-closure-search --no-coverage-search --no-microexon-search --sam-header ../out/tophat_pe_qsub/tmp/test_ref_genome.bwt.samheader.sam --ium-reads ../out/tophat_pe_qsub/tmp/left_kept_reads_seg1_unmapped.bam,../out/tophat_pe_qsub/tmp/left_kept_reads_seg2_unmapped.bam,../out/tophat_pe_qsub/tmp/left_kept_reads_seg3_unmapped.bam,../out/tophat_pe_qsub/tmp/right_kept_reads_seg1_unmapped.bam,../out/tophat_pe_qsub/tmp/right_kept_reads_seg2_unmapped.bam,../out/tophat_pe_qsub/tmp/right_kept_reads_seg3_unmapped.bam ../ref/test_ref.fa ../out/tophat_pe_qsub/tmp/segment.juncs ../out/tophat_pe_qsub/tmp/segment.insertions ../out/tophat_pe_qsub/tmp/segment.deletions ../out/tophat_pe_qsub/tmp/segment.fusions ../out/tophat_pe_qsub/tmp/left_kept_reads.bam ../out/tophat_pe_qsub/tmp/left_kept_reads.mapped.bam ../out/tophat_pe_qsub/tmp/left_kept_reads_seg1.bam,../out/tophat_pe_qsub/tmp/left_kept_reads_seg2.bam,../out/tophat_pe_qsub/tmp/left_kept_reads_seg3.bam ../out/tophat_pe_qsub/tmp/right_kept_reads.bam ../out/tophat_pe_qsub/tmp/right_kept_reads.mapped.bam ../out/tophat_pe_qsub/tmp/right_kept_reads_seg1.bam,../out/tophat_pe_qsub/tmp/right_kept_reads_seg2.bam,../out/tophat_pe_qsub/tmp/right_kept_reads_seg3.bam
#>juncs_db:
/share/pkg.7/tophat/2.1.1/install/bin/juncs_db 3 25 ../out/tophat_pe_qsub/tmp/segment.juncs /dev/null /dev/null /dev/null ../ref/test_ref.fa > ../out/tophat_pe_qsub/tmp/segment_juncs.fa
/share/pkg.7/bowtie2/2.4.2/install/bin/bowtie2-build ../out/tophat_pe_qsub/tmp/segment_juncs.fa ../out/tophat_pe_qsub/tmp/segment_juncs
#>map2juncs:
gzip -cd< ../out/tophat_pe_qsub/tmp/left_kept_reads_seg1.fq.z|/share/pkg.7/bowtie2/2.4.2/install/bin/bowtie2 -k 41 -N 1 -L 20 -p 4 --sam-no-hd -x ../out/tophat_pe_qsub/tmp/segment_juncs -|/share/pkg.7/tophat/2.1.1/install/bin/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 ../out/tophat_pe_qsub/tmp/left_kept_reads_seg1.to_spliced.bam.index --sam-header ../out/tophat_pe_qsub/tmp/segment_juncs.bwt.samheader.sam - ../out/tophat_pe_qsub/tmp/left_kept_reads_seg1.to_spliced.bam
gzip -cd< ../out/tophat_pe_qsub/tmp/left_kept_reads_seg2.fq.z|/share/pkg.7/bowtie2/2.4.2/install/bin/bowtie2 -k 41 -N 1 -L 20 -p 4 --sam-no-hd -x ../out/tophat_pe_qsub/tmp/segment_juncs -|/share/pkg.7/tophat/2.1.1/install/bin/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 ../out/tophat_pe_qsub/tmp/left_kept_reads_seg2.to_spliced.bam.index --sam-header ../out/tophat_pe_qsub/tmp/segment_juncs.bwt.samheader.sam - ../out/tophat_pe_qsub/tmp/left_kept_reads_seg2.to_spliced.bam
gzip -cd< ../out/tophat_pe_qsub/tmp/left_kept_reads_seg3.fq.z|/share/pkg.7/bowtie2/2.4.2/install/bin/bowtie2 -k 41 -N 1 -L 20 -p 4 --sam-no-hd -x ../out/tophat_pe_qsub/tmp/segment_juncs -|/share/pkg.7/tophat/2.1.1/install/bin/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 ../out/tophat_pe_qsub/tmp/left_kept_reads_seg3.to_spliced.bam.index --sam-header ../out/tophat_pe_qsub/tmp/segment_juncs.bwt.samheader.sam - ../out/tophat_pe_qsub/tmp/left_kept_reads_seg3.to_spliced.bam
/share/pkg.7/tophat/2.1.1/install/bin/long_spanning_reads --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir ../out/tophat_pe_qsub/ --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 -p4 --inner-dist-mean 50 --inner-dist-std-dev 20 --no-closure-search --no-coverage-search --no-microexon-search --sam-header ../out/tophat_pe_qsub/tmp/test_ref_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 ../ref/test_ref.fa ../out/tophat_pe_qsub/tmp/left_kept_reads.bam ../out/tophat_pe_qsub/tmp/segment.juncs /dev/null /dev/null /dev/null ../out/tophat_pe_qsub/tmp/left_kept_reads.candidates.bam ../out/tophat_pe_qsub/tmp/left_kept_reads_seg1.bam,../out/tophat_pe_qsub/tmp/left_kept_reads_seg2.bam,../out/tophat_pe_qsub/tmp/left_kept_reads_seg3.bam ../out/tophat_pe_qsub/tmp/left_kept_reads_seg1.to_spliced.bam,../out/tophat_pe_qsub/tmp/left_kept_reads_seg2.to_spliced.bam,../out/tophat_pe_qsub/tmp/left_kept_reads_seg3.to_spliced.bam
gzip -cd< ../out/tophat_pe_qsub/tmp/right_kept_reads_seg1.fq.z|/share/pkg.7/bowtie2/2.4.2/install/bin/bowtie2 -k 41 -N 1 -L 20 -p 4 --sam-no-hd -x ../out/tophat_pe_qsub/tmp/segment_juncs -|/share/pkg.7/tophat/2.1.1/install/bin/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 ../out/tophat_pe_qsub/tmp/right_kept_reads_seg1.to_spliced.bam.index --sam-header ../out/tophat_pe_qsub/tmp/segment_juncs.bwt.samheader.sam - ../out/tophat_pe_qsub/tmp/right_kept_reads_seg1.to_spliced.bam
gzip -cd< ../out/tophat_pe_qsub/tmp/right_kept_reads_seg2.fq.z|/share/pkg.7/bowtie2/2.4.2/install/bin/bowtie2 -k 41 -N 1 -L 20 -p 4 --sam-no-hd -x ../out/tophat_pe_qsub/tmp/segment_juncs -|/share/pkg.7/tophat/2.1.1/install/bin/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 ../out/tophat_pe_qsub/tmp/right_kept_reads_seg2.to_spliced.bam.index --sam-header ../out/tophat_pe_qsub/tmp/segment_juncs.bwt.samheader.sam - ../out/tophat_pe_qsub/tmp/right_kept_reads_seg2.to_spliced.bam
gzip -cd< ../out/tophat_pe_qsub/tmp/right_kept_reads_seg3.fq.z|/share/pkg.7/bowtie2/2.4.2/install/bin/bowtie2 -k 41 -N 1 -L 20 -p 4 --sam-no-hd -x ../out/tophat_pe_qsub/tmp/segment_juncs -|/share/pkg.7/tophat/2.1.1/install/bin/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 ../out/tophat_pe_qsub/tmp/right_kept_reads_seg3.to_spliced.bam.index --sam-header ../out/tophat_pe_qsub/tmp/segment_juncs.bwt.samheader.sam - ../out/tophat_pe_qsub/tmp/right_kept_reads_seg3.to_spliced.bam
/share/pkg.7/tophat/2.1.1/install/bin/long_spanning_reads --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir ../out/tophat_pe_qsub/ --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 -p4 --inner-dist-mean 50 --inner-dist-std-dev 20 --no-closure-search --no-coverage-search --no-microexon-search --sam-header ../out/tophat_pe_qsub/tmp/test_ref_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 ../ref/test_ref.fa ../out/tophat_pe_qsub/tmp/right_kept_reads.bam ../out/tophat_pe_qsub/tmp/segment.juncs /dev/null /dev/null /dev/null ../out/tophat_pe_qsub/tmp/right_kept_reads.candidates.bam ../out/tophat_pe_qsub/tmp/right_kept_reads_seg1.bam,../out/tophat_pe_qsub/tmp/right_kept_reads_seg2.bam,../out/tophat_pe_qsub/tmp/right_kept_reads_seg3.bam ../out/tophat_pe_qsub/tmp/right_kept_reads_seg1.to_spliced.bam,../out/tophat_pe_qsub/tmp/right_kept_reads_seg2.to_spliced.bam,../out/tophat_pe_qsub/tmp/right_kept_reads_seg3.to_spliced.bam
#>tophat_reports:
/share/pkg.7/tophat/2.1.1/install/bin/tophat_reports --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir ../out/tophat_pe_qsub/ --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 -p4 --inner-dist-mean 50 --inner-dist-std-dev 20 --no-closure-search --no-coverage-search --no-microexon-search --sam-header ../out/tophat_pe_qsub/tmp/test_ref_genome.bwt.samheader.sam --report-discordant-pair-alignments --report-mixed-alignments --samtools=/share/pkg.7/tophat/2.1.1/install/bin/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 ../ref/test_ref.fa ../out/tophat_pe_qsub/junctions.bed ../out/tophat_pe_qsub/insertions.bed ../out/tophat_pe_qsub/deletions.bed ../out/tophat_pe_qsub/fusions.out ../out/tophat_pe_qsub/tmp/accepted_hits ../out/tophat_pe_qsub/tmp/left_kept_reads.mapped.bam,../out/tophat_pe_qsub/tmp/left_kept_reads.candidates.bam ../out/tophat_pe_qsub/tmp/left_kept_reads.bam ../out/tophat_pe_qsub/tmp/right_kept_reads.mapped.bam,../out/tophat_pe_qsub/tmp/right_kept_reads.candidates.bam ../out/tophat_pe_qsub/tmp/right_kept_reads.bam
/share/pkg.7/tophat/2.1.1/install/bin/samtools_0.1.18 sort ../out/tophat_pe_qsub/tmp/accepted_hits0.bam ../out/tophat_pe_qsub/tmp/accepted_hits0_sorted
/share/pkg.7/tophat/2.1.1/install/bin/bam_merge -Q --sam-header ../out/tophat_pe_qsub/tmp/test_ref_genome.bwt.samheader.sam ../out/tophat_pe_qsub/unmapped.bam ../out/tophat_pe_qsub/tmp/unmapped_left_0.bam ../out/tophat_pe_qsub/tmp/unmapped_right_0.bam
#>alldone: