/usr/local/bioinfo/src/tophat/tophat-2.0.14/bin/tophat -o aln_tophat_mt --max-intron-length 5000 --mate-inner-dist 200 bowtie2-index/tomato_chr6 MT_rep1_1_Ch6.fastq.gz MT_rep1_2_Ch6.fastq.gz
#>prep_reads:
/usr/local/bioinfo/src/tophat/tophat-2.0.14/bin/prep_reads --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 5000 --min-isoform-fraction 0.15 --output-dir aln_tophat_mt/ --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 5000 --min-segment-intron 50 --max-segment-intron 5000 --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 --inner-dist-mean 200 --inner-dist-std-dev 20 --no-closure-search --no-coverage-search --no-microexon-search --aux-outfile=aln_tophat_mt/prep_reads.info --index-outfile=aln_tophat_mt/tmp/%side%_kept_reads.bam.index --sam-header=aln_tophat_mt/tmp/tomato_chr6_genome.bwt.samheader.sam --outfile=aln_tophat_mt/tmp/%side%_kept_reads.bam MT_rep1_1_Ch6.fastq.gz MT_rep1_2_Ch6.fastq.gz
#>map_start:
/usr/local/bioinfo/src/tophat/tophat-2.0.14/bin/bam2fastx --all aln_tophat_mt/tmp/left_kept_reads.bam|/usr/local/bioinfo/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 bowtie2-index/tomato_chr6 -|/usr/local/bioinfo/src/tophat/tophat-2.0.14/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 aln_tophat_mt/tmp/left_kept_reads.mapped.bam.index --sam-header aln_tophat_mt/tmp/tomato_chr6_genome.bwt.samheader.sam - aln_tophat_mt/tmp/left_kept_reads.mapped.bam aln_tophat_mt/tmp/left_kept_reads_unmapped.bam
#>map_segments:
gzip -cd< aln_tophat_mt/tmp/left_kept_reads_seg1.fq.z|/usr/local/bioinfo/bin/bowtie2 -k 41 -N 1 -L 20 -p 1 --sam-no-hd -x bowtie2-index/tomato_chr6 -|/usr/local/bioinfo/src/tophat/tophat-2.0.14/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 aln_tophat_mt/tmp/left_kept_reads_seg1.bam.index --sam-header aln_tophat_mt/tmp/tomato_chr6_genome.bwt.samheader.sam - aln_tophat_mt/tmp/left_kept_reads_seg1.bam aln_tophat_mt/tmp/left_kept_reads_seg1_unmapped.bam
gzip -cd< aln_tophat_mt/tmp/left_kept_reads_seg2.fq.z|/usr/local/bioinfo/bin/bowtie2 -k 41 -N 1 -L 20 -p 1 --sam-no-hd -x bowtie2-index/tomato_chr6 -|/usr/local/bioinfo/src/tophat/tophat-2.0.14/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 aln_tophat_mt/tmp/left_kept_reads_seg2.bam.index --sam-header aln_tophat_mt/tmp/tomato_chr6_genome.bwt.samheader.sam - aln_tophat_mt/tmp/left_kept_reads_seg2.bam aln_tophat_mt/tmp/left_kept_reads_seg2_unmapped.bam
gzip -cd< aln_tophat_mt/tmp/left_kept_reads_seg3.fq.z|/usr/local/bioinfo/bin/bowtie2 -k 41 -N 1 -L 20 -p 1 --sam-no-hd -x bowtie2-index/tomato_chr6 -|/usr/local/bioinfo/src/tophat/tophat-2.0.14/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 aln_tophat_mt/tmp/left_kept_reads_seg3.bam.index --sam-header aln_tophat_mt/tmp/tomato_chr6_genome.bwt.samheader.sam - aln_tophat_mt/tmp/left_kept_reads_seg3.bam aln_tophat_mt/tmp/left_kept_reads_seg3_unmapped.bam
gzip -cd< aln_tophat_mt/tmp/left_kept_reads_seg4.fq.z|/usr/local/bioinfo/bin/bowtie2 -k 41 -N 1 -L 20 -p 1 --sam-no-hd -x bowtie2-index/tomato_chr6 -|/usr/local/bioinfo/src/tophat/tophat-2.0.14/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 aln_tophat_mt/tmp/left_kept_reads_seg4.bam.index --sam-header aln_tophat_mt/tmp/tomato_chr6_genome.bwt.samheader.sam - aln_tophat_mt/tmp/left_kept_reads_seg4.bam aln_tophat_mt/tmp/left_kept_reads_seg4_unmapped.bam
/usr/local/bioinfo/src/tophat/tophat-2.0.14/bin/bam2fastx --all aln_tophat_mt/tmp/right_kept_reads.bam|/usr/local/bioinfo/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 bowtie2-index/tomato_chr6 -|/usr/local/bioinfo/src/tophat/tophat-2.0.14/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 aln_tophat_mt/tmp/right_kept_reads.mapped.bam.index --sam-header aln_tophat_mt/tmp/tomato_chr6_genome.bwt.samheader.sam - aln_tophat_mt/tmp/right_kept_reads.mapped.bam aln_tophat_mt/tmp/right_kept_reads_unmapped.bam
#>map_segments:
gzip -cd< aln_tophat_mt/tmp/right_kept_reads_seg1.fq.z|/usr/local/bioinfo/bin/bowtie2 -k 41 -N 1 -L 20 -p 1 --sam-no-hd -x bowtie2-index/tomato_chr6 -|/usr/local/bioinfo/src/tophat/tophat-2.0.14/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 aln_tophat_mt/tmp/right_kept_reads_seg1.bam.index --sam-header aln_tophat_mt/tmp/tomato_chr6_genome.bwt.samheader.sam - aln_tophat_mt/tmp/right_kept_reads_seg1.bam aln_tophat_mt/tmp/right_kept_reads_seg1_unmapped.bam
gzip -cd< aln_tophat_mt/tmp/right_kept_reads_seg2.fq.z|/usr/local/bioinfo/bin/bowtie2 -k 41 -N 1 -L 20 -p 1 --sam-no-hd -x bowtie2-index/tomato_chr6 -|/usr/local/bioinfo/src/tophat/tophat-2.0.14/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 aln_tophat_mt/tmp/right_kept_reads_seg2.bam.index --sam-header aln_tophat_mt/tmp/tomato_chr6_genome.bwt.samheader.sam - aln_tophat_mt/tmp/right_kept_reads_seg2.bam aln_tophat_mt/tmp/right_kept_reads_seg2_unmapped.bam
gzip -cd< aln_tophat_mt/tmp/right_kept_reads_seg3.fq.z|/usr/local/bioinfo/bin/bowtie2 -k 41 -N 1 -L 20 -p 1 --sam-no-hd -x bowtie2-index/tomato_chr6 -|/usr/local/bioinfo/src/tophat/tophat-2.0.14/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 aln_tophat_mt/tmp/right_kept_reads_seg3.bam.index --sam-header aln_tophat_mt/tmp/tomato_chr6_genome.bwt.samheader.sam - aln_tophat_mt/tmp/right_kept_reads_seg3.bam aln_tophat_mt/tmp/right_kept_reads_seg3_unmapped.bam
gzip -cd< aln_tophat_mt/tmp/right_kept_reads_seg4.fq.z|/usr/local/bioinfo/bin/bowtie2 -k 41 -N 1 -L 20 -p 1 --sam-no-hd -x bowtie2-index/tomato_chr6 -|/usr/local/bioinfo/src/tophat/tophat-2.0.14/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 aln_tophat_mt/tmp/right_kept_reads_seg4.bam.index --sam-header aln_tophat_mt/tmp/tomato_chr6_genome.bwt.samheader.sam - aln_tophat_mt/tmp/right_kept_reads_seg4.bam aln_tophat_mt/tmp/right_kept_reads_seg4_unmapped.bam
#>find_juncs:
/usr/local/bioinfo/src/tophat/tophat-2.0.14/bin/segment_juncs --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 5000 --min-isoform-fraction 0.15 --output-dir aln_tophat_mt/ --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 5000 --min-segment-intron 50 --max-segment-intron 5000 --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 --inner-dist-mean 200 --inner-dist-std-dev 20 --no-closure-search --no-coverage-search --no-microexon-search --sam-header aln_tophat_mt/tmp/tomato_chr6_genome.bwt.samheader.sam --ium-reads aln_tophat_mt/tmp/left_kept_reads_seg1_unmapped.bam,aln_tophat_mt/tmp/left_kept_reads_seg2_unmapped.bam,aln_tophat_mt/tmp/left_kept_reads_seg3_unmapped.bam,aln_tophat_mt/tmp/left_kept_reads_seg4_unmapped.bam,aln_tophat_mt/tmp/right_kept_reads_seg1_unmapped.bam,aln_tophat_mt/tmp/right_kept_reads_seg2_unmapped.bam,aln_tophat_mt/tmp/right_kept_reads_seg3_unmapped.bam,aln_tophat_mt/tmp/right_kept_reads_seg4_unmapped.bam aln_tophat_mt/tmp/tomato_chr6.fa aln_tophat_mt/tmp/segment.juncs aln_tophat_mt/tmp/segment.insertions aln_tophat_mt/tmp/segment.deletions aln_tophat_mt/tmp/segment.fusions aln_tophat_mt/tmp/left_kept_reads.bam aln_tophat_mt/tmp/left_kept_reads.mapped.bam aln_tophat_mt/tmp/left_kept_reads_seg1.bam,aln_tophat_mt/tmp/left_kept_reads_seg2.bam,aln_tophat_mt/tmp/left_kept_reads_seg3.bam,aln_tophat_mt/tmp/left_kept_reads_seg4.bam aln_tophat_mt/tmp/right_kept_reads.bam aln_tophat_mt/tmp/right_kept_reads.mapped.bam aln_tophat_mt/tmp/right_kept_reads_seg1.bam,aln_tophat_mt/tmp/right_kept_reads_seg2.bam,aln_tophat_mt/tmp/right_kept_reads_seg3.bam,aln_tophat_mt/tmp/right_kept_reads_seg4.bam
#>juncs_db:
/usr/local/bioinfo/src/tophat/tophat-2.0.14/bin/juncs_db 3 26 aln_tophat_mt/tmp/segment.juncs /dev/null /dev/null /dev/null aln_tophat_mt/tmp/tomato_chr6.fa > aln_tophat_mt/tmp/segment_juncs.fa
/usr/local/bioinfo/bin/bowtie2-build aln_tophat_mt/tmp/segment_juncs.fa aln_tophat_mt/tmp/segment_juncs
#>map2juncs:
gzip -cd< aln_tophat_mt/tmp/left_kept_reads_seg1.fq.z|/usr/local/bioinfo/bin/bowtie2 -k 41 -N 1 -L 20 -p 1 --sam-no-hd -x aln_tophat_mt/tmp/segment_juncs -|/usr/local/bioinfo/src/tophat/tophat-2.0.14/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 aln_tophat_mt/tmp/left_kept_reads_seg1.to_spliced.bam.index --sam-header aln_tophat_mt/tmp/segment_juncs.bwt.samheader.sam - aln_tophat_mt/tmp/left_kept_reads_seg1.to_spliced.bam
gzip -cd< aln_tophat_mt/tmp/left_kept_reads_seg2.fq.z|/usr/local/bioinfo/bin/bowtie2 -k 41 -N 1 -L 20 -p 1 --sam-no-hd -x aln_tophat_mt/tmp/segment_juncs -|/usr/local/bioinfo/src/tophat/tophat-2.0.14/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 aln_tophat_mt/tmp/left_kept_reads_seg2.to_spliced.bam.index --sam-header aln_tophat_mt/tmp/segment_juncs.bwt.samheader.sam - aln_tophat_mt/tmp/left_kept_reads_seg2.to_spliced.bam
gzip -cd< aln_tophat_mt/tmp/left_kept_reads_seg3.fq.z|/usr/local/bioinfo/bin/bowtie2 -k 41 -N 1 -L 20 -p 1 --sam-no-hd -x aln_tophat_mt/tmp/segment_juncs -|/usr/local/bioinfo/src/tophat/tophat-2.0.14/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 aln_tophat_mt/tmp/left_kept_reads_seg3.to_spliced.bam.index --sam-header aln_tophat_mt/tmp/segment_juncs.bwt.samheader.sam - aln_tophat_mt/tmp/left_kept_reads_seg3.to_spliced.bam
gzip -cd< aln_tophat_mt/tmp/left_kept_reads_seg4.fq.z|/usr/local/bioinfo/bin/bowtie2 -k 41 -N 1 -L 20 -p 1 --sam-no-hd -x aln_tophat_mt/tmp/segment_juncs -|/usr/local/bioinfo/src/tophat/tophat-2.0.14/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 aln_tophat_mt/tmp/left_kept_reads_seg4.to_spliced.bam.index --sam-header aln_tophat_mt/tmp/segment_juncs.bwt.samheader.sam - aln_tophat_mt/tmp/left_kept_reads_seg4.to_spliced.bam
/usr/local/bioinfo/src/tophat/tophat-2.0.14/bin/long_spanning_reads --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 5000 --min-isoform-fraction 0.15 --output-dir aln_tophat_mt/ --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 5000 --min-segment-intron 50 --max-segment-intron 5000 --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 --inner-dist-mean 200 --inner-dist-std-dev 20 --no-closure-search --no-coverage-search --no-microexon-search --sam-header aln_tophat_mt/tmp/tomato_chr6_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 aln_tophat_mt/tmp/tomato_chr6.fa aln_tophat_mt/tmp/left_kept_reads.bam aln_tophat_mt/tmp/segment.juncs aln_tophat_mt/tmp/segment.insertions aln_tophat_mt/tmp/segment.deletions /dev/null aln_tophat_mt/tmp/left_kept_reads.candidates.bam aln_tophat_mt/tmp/left_kept_reads_seg1.bam,aln_tophat_mt/tmp/left_kept_reads_seg2.bam,aln_tophat_mt/tmp/left_kept_reads_seg3.bam,aln_tophat_mt/tmp/left_kept_reads_seg4.bam aln_tophat_mt/tmp/left_kept_reads_seg1.to_spliced.bam,aln_tophat_mt/tmp/left_kept_reads_seg2.to_spliced.bam,aln_tophat_mt/tmp/left_kept_reads_seg3.to_spliced.bam,aln_tophat_mt/tmp/left_kept_reads_seg4.to_spliced.bam
gzip -cd< aln_tophat_mt/tmp/right_kept_reads_seg1.fq.z|/usr/local/bioinfo/bin/bowtie2 -k 41 -N 1 -L 20 -p 1 --sam-no-hd -x aln_tophat_mt/tmp/segment_juncs -|/usr/local/bioinfo/src/tophat/tophat-2.0.14/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 aln_tophat_mt/tmp/right_kept_reads_seg1.to_spliced.bam.index --sam-header aln_tophat_mt/tmp/segment_juncs.bwt.samheader.sam - aln_tophat_mt/tmp/right_kept_reads_seg1.to_spliced.bam
gzip -cd< aln_tophat_mt/tmp/right_kept_reads_seg2.fq.z|/usr/local/bioinfo/bin/bowtie2 -k 41 -N 1 -L 20 -p 1 --sam-no-hd -x aln_tophat_mt/tmp/segment_juncs -|/usr/local/bioinfo/src/tophat/tophat-2.0.14/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 aln_tophat_mt/tmp/right_kept_reads_seg2.to_spliced.bam.index --sam-header aln_tophat_mt/tmp/segment_juncs.bwt.samheader.sam - aln_tophat_mt/tmp/right_kept_reads_seg2.to_spliced.bam
gzip -cd< aln_tophat_mt/tmp/right_kept_reads_seg3.fq.z|/usr/local/bioinfo/bin/bowtie2 -k 41 -N 1 -L 20 -p 1 --sam-no-hd -x aln_tophat_mt/tmp/segment_juncs -|/usr/local/bioinfo/src/tophat/tophat-2.0.14/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 aln_tophat_mt/tmp/right_kept_reads_seg3.to_spliced.bam.index --sam-header aln_tophat_mt/tmp/segment_juncs.bwt.samheader.sam - aln_tophat_mt/tmp/right_kept_reads_seg3.to_spliced.bam
gzip -cd< aln_tophat_mt/tmp/right_kept_reads_seg4.fq.z|/usr/local/bioinfo/bin/bowtie2 -k 41 -N 1 -L 20 -p 1 --sam-no-hd -x aln_tophat_mt/tmp/segment_juncs -|/usr/local/bioinfo/src/tophat/tophat-2.0.14/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 aln_tophat_mt/tmp/right_kept_reads_seg4.to_spliced.bam.index --sam-header aln_tophat_mt/tmp/segment_juncs.bwt.samheader.sam - aln_tophat_mt/tmp/right_kept_reads_seg4.to_spliced.bam
/usr/local/bioinfo/src/tophat/tophat-2.0.14/bin/long_spanning_reads --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 5000 --min-isoform-fraction 0.15 --output-dir aln_tophat_mt/ --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 5000 --min-segment-intron 50 --max-segment-intron 5000 --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 --inner-dist-mean 200 --inner-dist-std-dev 20 --no-closure-search --no-coverage-search --no-microexon-search --sam-header aln_tophat_mt/tmp/tomato_chr6_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 aln_tophat_mt/tmp/tomato_chr6.fa aln_tophat_mt/tmp/right_kept_reads.bam aln_tophat_mt/tmp/segment.juncs aln_tophat_mt/tmp/segment.insertions aln_tophat_mt/tmp/segment.deletions /dev/null aln_tophat_mt/tmp/right_kept_reads.candidates.bam aln_tophat_mt/tmp/right_kept_reads_seg1.bam,aln_tophat_mt/tmp/right_kept_reads_seg2.bam,aln_tophat_mt/tmp/right_kept_reads_seg3.bam,aln_tophat_mt/tmp/right_kept_reads_seg4.bam aln_tophat_mt/tmp/right_kept_reads_seg1.to_spliced.bam,aln_tophat_mt/tmp/right_kept_reads_seg2.to_spliced.bam,aln_tophat_mt/tmp/right_kept_reads_seg3.to_spliced.bam,aln_tophat_mt/tmp/right_kept_reads_seg4.to_spliced.bam
#>tophat_reports:
/usr/local/bioinfo/src/tophat/tophat-2.0.14/bin/tophat_reports --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 5000 --min-isoform-fraction 0.15 --output-dir aln_tophat_mt/ --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 5000 --min-segment-intron 50 --max-segment-intron 5000 --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 --inner-dist-mean 200 --inner-dist-std-dev 20 --no-closure-search --no-coverage-search --no-microexon-search --sam-header aln_tophat_mt/tmp/tomato_chr6_genome.bwt.samheader.sam --report-discordant-pair-alignments --report-mixed-alignments --samtools=/usr/local/bioinfo/src/tophat/tophat-2.0.14/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 aln_tophat_mt/tmp/tomato_chr6.fa aln_tophat_mt/junctions.bed aln_tophat_mt/insertions.bed aln_tophat_mt/deletions.bed aln_tophat_mt/fusions.out aln_tophat_mt/tmp/accepted_hits aln_tophat_mt/tmp/left_kept_reads.mapped.bam,aln_tophat_mt/tmp/left_kept_reads.candidates.bam aln_tophat_mt/tmp/left_kept_reads.bam aln_tophat_mt/tmp/right_kept_reads.mapped.bam,aln_tophat_mt/tmp/right_kept_reads.candidates.bam aln_tophat_mt/tmp/right_kept_reads.bam
/usr/local/bioinfo/src/tophat/tophat-2.0.14/bin/samtools_0.1.18 sort aln_tophat_mt/tmp/accepted_hits0.bam aln_tophat_mt/tmp/accepted_hits0_sorted
/usr/local/bioinfo/src/tophat/tophat-2.0.14/bin/bam_merge -Q --sam-header aln_tophat_mt/tmp/tomato_chr6_genome.bwt.samheader.sam aln_tophat_mt/unmapped.bam aln_tophat_mt/tmp/unmapped_left_0.bam aln_tophat_mt/tmp/unmapped_right_0.bam
#>alldone: