/data/results/tools/align/tophat-2.1.1.Linux_x86_64/tophat -o wt0h1_v2 -p 18 --library-type fr-unstranded -g 1 /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome wt01_R1_trm_1.fastq.gz wt01_R2_trm_2.fastq.gz
#>prep_reads:
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.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 wt0h1_v2/ --max-multihits 1 --max-seg-multihits 10 --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 -p18 --inner-dist-mean 50 --inner-dist-std-dev 20 --no-closure-search --no-coverage-search --no-microexon-search --library-type fr-unstranded --aux-outfile=wt0h1_v2/prep_reads.info --index-outfile=wt0h1_v2/tmp/%side%_kept_reads.bam.index --sam-header=wt0h1_v2/tmp/genome_genome.bwt.samheader.sam --outfile=wt0h1_v2/tmp/%side%_kept_reads.bam wt01_R1_trm_1.fastq.gz wt01_R2_trm_2.fastq.gz
#>map_start:
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.Linux_x86_64/bam2fastx --all wt0h1_v2/tmp/left_kept_reads.bam|/data/results/tools/align/bowtie2-2.3.2/bowtie2 -k 1 -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 18 --sam-no-hd -x /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome -|/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.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 wt0h1_v2/tmp/left_kept_reads.mapped.bam.index --sam-header wt0h1_v2/tmp/genome_genome.bwt.samheader.sam - wt0h1_v2/tmp/left_kept_reads.mapped.bam wt0h1_v2/tmp/left_kept_reads_unmapped.bam
#>map_segments:
gzip -cd< wt0h1_v2/tmp/left_kept_reads_seg1.fq.z|/data/results/tools/align/bowtie2-2.3.2/bowtie2 -k 11 -N 1 -L 20 -p 18 --sam-no-hd -x /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome -|/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.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 wt0h1_v2/tmp/left_kept_reads_seg1.bam.index --sam-header wt0h1_v2/tmp/genome_genome.bwt.samheader.sam - wt0h1_v2/tmp/left_kept_reads_seg1.bam wt0h1_v2/tmp/left_kept_reads_seg1_unmapped.bam
gzip -cd< wt0h1_v2/tmp/left_kept_reads_seg2.fq.z|/data/results/tools/align/bowtie2-2.3.2/bowtie2 -k 11 -N 1 -L 20 -p 18 --sam-no-hd -x /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome -|/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.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 wt0h1_v2/tmp/left_kept_reads_seg2.bam.index --sam-header wt0h1_v2/tmp/genome_genome.bwt.samheader.sam - wt0h1_v2/tmp/left_kept_reads_seg2.bam wt0h1_v2/tmp/left_kept_reads_seg2_unmapped.bam
gzip -cd< wt0h1_v2/tmp/left_kept_reads_seg3.fq.z|/data/results/tools/align/bowtie2-2.3.2/bowtie2 -k 11 -N 1 -L 20 -p 18 --sam-no-hd -x /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome -|/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.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 wt0h1_v2/tmp/left_kept_reads_seg3.bam.index --sam-header wt0h1_v2/tmp/genome_genome.bwt.samheader.sam - wt0h1_v2/tmp/left_kept_reads_seg3.bam wt0h1_v2/tmp/left_kept_reads_seg3_unmapped.bam
gzip -cd< wt0h1_v2/tmp/left_kept_reads_seg4.fq.z|/data/results/tools/align/bowtie2-2.3.2/bowtie2 -k 11 -N 1 -L 20 -p 18 --sam-no-hd -x /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome -|/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.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 wt0h1_v2/tmp/left_kept_reads_seg4.bam.index --sam-header wt0h1_v2/tmp/genome_genome.bwt.samheader.sam - wt0h1_v2/tmp/left_kept_reads_seg4.bam wt0h1_v2/tmp/left_kept_reads_seg4_unmapped.bam
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.Linux_x86_64/bam2fastx --all wt0h1_v2/tmp/right_kept_reads.bam|/data/results/tools/align/bowtie2-2.3.2/bowtie2 -k 1 -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 18 --sam-no-hd -x /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome -|/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.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 wt0h1_v2/tmp/right_kept_reads.mapped.bam.index --sam-header wt0h1_v2/tmp/genome_genome.bwt.samheader.sam - wt0h1_v2/tmp/right_kept_reads.mapped.bam wt0h1_v2/tmp/right_kept_reads_unmapped.bam
#>map_segments:
gzip -cd< wt0h1_v2/tmp/right_kept_reads_seg1.fq.z|/data/results/tools/align/bowtie2-2.3.2/bowtie2 -k 11 -N 1 -L 20 -p 18 --sam-no-hd -x /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome -|/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.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 wt0h1_v2/tmp/right_kept_reads_seg1.bam.index --sam-header wt0h1_v2/tmp/genome_genome.bwt.samheader.sam - wt0h1_v2/tmp/right_kept_reads_seg1.bam wt0h1_v2/tmp/right_kept_reads_seg1_unmapped.bam
gzip -cd< wt0h1_v2/tmp/right_kept_reads_seg2.fq.z|/data/results/tools/align/bowtie2-2.3.2/bowtie2 -k 11 -N 1 -L 20 -p 18 --sam-no-hd -x /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome -|/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.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 wt0h1_v2/tmp/right_kept_reads_seg2.bam.index --sam-header wt0h1_v2/tmp/genome_genome.bwt.samheader.sam - wt0h1_v2/tmp/right_kept_reads_seg2.bam wt0h1_v2/tmp/right_kept_reads_seg2_unmapped.bam
gzip -cd< wt0h1_v2/tmp/right_kept_reads_seg3.fq.z|/data/results/tools/align/bowtie2-2.3.2/bowtie2 -k 11 -N 1 -L 20 -p 18 --sam-no-hd -x /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome -|/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.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 wt0h1_v2/tmp/right_kept_reads_seg3.bam.index --sam-header wt0h1_v2/tmp/genome_genome.bwt.samheader.sam - wt0h1_v2/tmp/right_kept_reads_seg3.bam wt0h1_v2/tmp/right_kept_reads_seg3_unmapped.bam
gzip -cd< wt0h1_v2/tmp/right_kept_reads_seg4.fq.z|/data/results/tools/align/bowtie2-2.3.2/bowtie2 -k 11 -N 1 -L 20 -p 18 --sam-no-hd -x /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome -|/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.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 wt0h1_v2/tmp/right_kept_reads_seg4.bam.index --sam-header wt0h1_v2/tmp/genome_genome.bwt.samheader.sam - wt0h1_v2/tmp/right_kept_reads_seg4.bam wt0h1_v2/tmp/right_kept_reads_seg4_unmapped.bam
#>find_juncs:
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.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 wt0h1_v2/ --max-multihits 1 --max-seg-multihits 10 --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 -p18 --inner-dist-mean 50 --inner-dist-std-dev 20 --no-closure-search --no-coverage-search --no-microexon-search --library-type fr-unstranded --sam-header wt0h1_v2/tmp/genome_genome.bwt.samheader.sam --ium-reads wt0h1_v2/tmp/left_kept_reads_seg1_unmapped.bam,wt0h1_v2/tmp/left_kept_reads_seg2_unmapped.bam,wt0h1_v2/tmp/left_kept_reads_seg3_unmapped.bam,wt0h1_v2/tmp/left_kept_reads_seg4_unmapped.bam,wt0h1_v2/tmp/right_kept_reads_seg1_unmapped.bam,wt0h1_v2/tmp/right_kept_reads_seg2_unmapped.bam,wt0h1_v2/tmp/right_kept_reads_seg3_unmapped.bam,wt0h1_v2/tmp/right_kept_reads_seg4_unmapped.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome.fa wt0h1_v2/tmp/segment.juncs wt0h1_v2/tmp/segment.insertions wt0h1_v2/tmp/segment.deletions wt0h1_v2/tmp/segment.fusions wt0h1_v2/tmp/left_kept_reads.bam wt0h1_v2/tmp/left_kept_reads.mapped.bam wt0h1_v2/tmp/left_kept_reads_seg1.bam,wt0h1_v2/tmp/left_kept_reads_seg2.bam,wt0h1_v2/tmp/left_kept_reads_seg3.bam,wt0h1_v2/tmp/left_kept_reads_seg4.bam wt0h1_v2/tmp/right_kept_reads.bam wt0h1_v2/tmp/right_kept_reads.mapped.bam wt0h1_v2/tmp/right_kept_reads_seg1.bam,wt0h1_v2/tmp/right_kept_reads_seg2.bam,wt0h1_v2/tmp/right_kept_reads_seg3.bam,wt0h1_v2/tmp/right_kept_reads_seg4.bam
#>juncs_db:
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.Linux_x86_64/juncs_db 3 25 wt0h1_v2/tmp/segment.juncs /dev/null /dev/null /dev/null /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome.fa > wt0h1_v2/tmp/segment_juncs.fa
/data/results/tools/align/bowtie2-2.3.2/bowtie2-build wt0h1_v2/tmp/segment_juncs.fa wt0h1_v2/tmp/segment_juncs
#>map2juncs:
gzip -cd< wt0h1_v2/tmp/left_kept_reads_seg1.fq.z|/data/results/tools/align/bowtie2-2.3.2/bowtie2 -k 11 -N 1 -L 20 -p 18 --sam-no-hd -x wt0h1_v2/tmp/segment_juncs -|/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.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 wt0h1_v2/tmp/left_kept_reads_seg1.to_spliced.bam.index --sam-header wt0h1_v2/tmp/segment_juncs.bwt.samheader.sam - wt0h1_v2/tmp/left_kept_reads_seg1.to_spliced.bam
gzip -cd< wt0h1_v2/tmp/left_kept_reads_seg2.fq.z|/data/results/tools/align/bowtie2-2.3.2/bowtie2 -k 11 -N 1 -L 20 -p 18 --sam-no-hd -x wt0h1_v2/tmp/segment_juncs -|/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.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 wt0h1_v2/tmp/left_kept_reads_seg2.to_spliced.bam.index --sam-header wt0h1_v2/tmp/segment_juncs.bwt.samheader.sam - wt0h1_v2/tmp/left_kept_reads_seg2.to_spliced.bam
gzip -cd< wt0h1_v2/tmp/left_kept_reads_seg3.fq.z|/data/results/tools/align/bowtie2-2.3.2/bowtie2 -k 11 -N 1 -L 20 -p 18 --sam-no-hd -x wt0h1_v2/tmp/segment_juncs -|/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.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 wt0h1_v2/tmp/left_kept_reads_seg3.to_spliced.bam.index --sam-header wt0h1_v2/tmp/segment_juncs.bwt.samheader.sam - wt0h1_v2/tmp/left_kept_reads_seg3.to_spliced.bam
gzip -cd< wt0h1_v2/tmp/left_kept_reads_seg4.fq.z|/data/results/tools/align/bowtie2-2.3.2/bowtie2 -k 11 -N 1 -L 20 -p 18 --sam-no-hd -x wt0h1_v2/tmp/segment_juncs -|/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.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 wt0h1_v2/tmp/left_kept_reads_seg4.to_spliced.bam.index --sam-header wt0h1_v2/tmp/segment_juncs.bwt.samheader.sam - wt0h1_v2/tmp/left_kept_reads_seg4.to_spliced.bam
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.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 wt0h1_v2/ --max-multihits 1 --max-seg-multihits 10 --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 -p18 --inner-dist-mean 50 --inner-dist-std-dev 20 --no-closure-search --no-coverage-search --no-microexon-search --library-type fr-unstranded --sam-header wt0h1_v2/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 /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome.fa wt0h1_v2/tmp/left_kept_reads.bam wt0h1_v2/tmp/segment.juncs wt0h1_v2/tmp/segment.insertions wt0h1_v2/tmp/segment.deletions /dev/null wt0h1_v2/tmp/left_kept_reads.candidates.bam wt0h1_v2/tmp/left_kept_reads_seg1.bam,wt0h1_v2/tmp/left_kept_reads_seg2.bam,wt0h1_v2/tmp/left_kept_reads_seg3.bam,wt0h1_v2/tmp/left_kept_reads_seg4.bam wt0h1_v2/tmp/left_kept_reads_seg1.to_spliced.bam,wt0h1_v2/tmp/left_kept_reads_seg2.to_spliced.bam,wt0h1_v2/tmp/left_kept_reads_seg3.to_spliced.bam,wt0h1_v2/tmp/left_kept_reads_seg4.to_spliced.bam
gzip -cd< wt0h1_v2/tmp/right_kept_reads_seg1.fq.z|/data/results/tools/align/bowtie2-2.3.2/bowtie2 -k 11 -N 1 -L 20 -p 18 --sam-no-hd -x wt0h1_v2/tmp/segment_juncs -|/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.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 wt0h1_v2/tmp/right_kept_reads_seg1.to_spliced.bam.index --sam-header wt0h1_v2/tmp/segment_juncs.bwt.samheader.sam - wt0h1_v2/tmp/right_kept_reads_seg1.to_spliced.bam
gzip -cd< wt0h1_v2/tmp/right_kept_reads_seg2.fq.z|/data/results/tools/align/bowtie2-2.3.2/bowtie2 -k 11 -N 1 -L 20 -p 18 --sam-no-hd -x wt0h1_v2/tmp/segment_juncs -|/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.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 wt0h1_v2/tmp/right_kept_reads_seg2.to_spliced.bam.index --sam-header wt0h1_v2/tmp/segment_juncs.bwt.samheader.sam - wt0h1_v2/tmp/right_kept_reads_seg2.to_spliced.bam
gzip -cd< wt0h1_v2/tmp/right_kept_reads_seg3.fq.z|/data/results/tools/align/bowtie2-2.3.2/bowtie2 -k 11 -N 1 -L 20 -p 18 --sam-no-hd -x wt0h1_v2/tmp/segment_juncs -|/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.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 wt0h1_v2/tmp/right_kept_reads_seg3.to_spliced.bam.index --sam-header wt0h1_v2/tmp/segment_juncs.bwt.samheader.sam - wt0h1_v2/tmp/right_kept_reads_seg3.to_spliced.bam
gzip -cd< wt0h1_v2/tmp/right_kept_reads_seg4.fq.z|/data/results/tools/align/bowtie2-2.3.2/bowtie2 -k 11 -N 1 -L 20 -p 18 --sam-no-hd -x wt0h1_v2/tmp/segment_juncs -|/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.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 wt0h1_v2/tmp/right_kept_reads_seg4.to_spliced.bam.index --sam-header wt0h1_v2/tmp/segment_juncs.bwt.samheader.sam - wt0h1_v2/tmp/right_kept_reads_seg4.to_spliced.bam
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.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 wt0h1_v2/ --max-multihits 1 --max-seg-multihits 10 --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 -p18 --inner-dist-mean 50 --inner-dist-std-dev 20 --no-closure-search --no-coverage-search --no-microexon-search --library-type fr-unstranded --sam-header wt0h1_v2/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 /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome.fa wt0h1_v2/tmp/right_kept_reads.bam wt0h1_v2/tmp/segment.juncs wt0h1_v2/tmp/segment.insertions wt0h1_v2/tmp/segment.deletions /dev/null wt0h1_v2/tmp/right_kept_reads.candidates.bam wt0h1_v2/tmp/right_kept_reads_seg1.bam,wt0h1_v2/tmp/right_kept_reads_seg2.bam,wt0h1_v2/tmp/right_kept_reads_seg3.bam,wt0h1_v2/tmp/right_kept_reads_seg4.bam wt0h1_v2/tmp/right_kept_reads_seg1.to_spliced.bam,wt0h1_v2/tmp/right_kept_reads_seg2.to_spliced.bam,wt0h1_v2/tmp/right_kept_reads_seg3.to_spliced.bam,wt0h1_v2/tmp/right_kept_reads_seg4.to_spliced.bam
#>tophat_reports:
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.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 wt0h1_v2/ --max-multihits 1 --max-seg-multihits 10 --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 -p18 --inner-dist-mean 50 --inner-dist-std-dev 20 --no-closure-search --no-coverage-search --no-microexon-search --library-type fr-unstranded --sam-header wt0h1_v2/tmp/genome_genome.bwt.samheader.sam --report-discordant-pair-alignments --report-mixed-alignments --samtools=/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.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 /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome.fa wt0h1_v2/junctions.bed wt0h1_v2/insertions.bed wt0h1_v2/deletions.bed wt0h1_v2/fusions.out wt0h1_v2/tmp/accepted_hits wt0h1_v2/tmp/left_kept_reads.mapped.bam,wt0h1_v2/tmp/left_kept_reads.candidates wt0h1_v2/tmp/left_kept_reads.bam wt0h1_v2/tmp/right_kept_reads.mapped.bam,wt0h1_v2/tmp/right_kept_reads.candidates wt0h1_v2/tmp/right_kept_reads.bam
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.Linux_x86_64/samtools_0.1.18 sort wt0h1_v2/tmp/accepted_hits0.bam wt0h1_v2/tmp/accepted_hits0_sorted
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.Linux_x86_64/samtools_0.1.18 sort wt0h1_v2/tmp/accepted_hits1.bam wt0h1_v2/tmp/accepted_hits1_sorted
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.Linux_x86_64/samtools_0.1.18 sort wt0h1_v2/tmp/accepted_hits2.bam wt0h1_v2/tmp/accepted_hits2_sorted
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.Linux_x86_64/samtools_0.1.18 sort wt0h1_v2/tmp/accepted_hits3.bam wt0h1_v2/tmp/accepted_hits3_sorted
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.Linux_x86_64/samtools_0.1.18 sort wt0h1_v2/tmp/accepted_hits4.bam wt0h1_v2/tmp/accepted_hits4_sorted
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.Linux_x86_64/samtools_0.1.18 sort wt0h1_v2/tmp/accepted_hits5.bam wt0h1_v2/tmp/accepted_hits5_sorted
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.Linux_x86_64/samtools_0.1.18 sort wt0h1_v2/tmp/accepted_hits6.bam wt0h1_v2/tmp/accepted_hits6_sorted
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.Linux_x86_64/samtools_0.1.18 sort wt0h1_v2/tmp/accepted_hits7.bam wt0h1_v2/tmp/accepted_hits7_sorted
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.Linux_x86_64/samtools_0.1.18 sort wt0h1_v2/tmp/accepted_hits8.bam wt0h1_v2/tmp/accepted_hits8_sorted
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.Linux_x86_64/samtools_0.1.18 sort wt0h1_v2/tmp/accepted_hits9.bam wt0h1_v2/tmp/accepted_hits9_sorted
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.Linux_x86_64/samtools_0.1.18 sort wt0h1_v2/tmp/accepted_hits10.bam wt0h1_v2/tmp/accepted_hits10_sorted
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.Linux_x86_64/samtools_0.1.18 sort wt0h1_v2/tmp/accepted_hits11.bam wt0h1_v2/tmp/accepted_hits11_sorted
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.Linux_x86_64/samtools_0.1.18 sort wt0h1_v2/tmp/accepted_hits12.bam wt0h1_v2/tmp/accepted_hits12_sorted
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.Linux_x86_64/samtools_0.1.18 sort wt0h1_v2/tmp/accepted_hits13.bam wt0h1_v2/tmp/accepted_hits13_sorted
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.Linux_x86_64/samtools_0.1.18 sort wt0h1_v2/tmp/accepted_hits14.bam wt0h1_v2/tmp/accepted_hits14_sorted
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.Linux_x86_64/samtools_0.1.18 sort wt0h1_v2/tmp/accepted_hits15.bam wt0h1_v2/tmp/accepted_hits15_sorted
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.Linux_x86_64/samtools_0.1.18 sort wt0h1_v2/tmp/accepted_hits16.bam wt0h1_v2/tmp/accepted_hits16_sorted
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.Linux_x86_64/samtools_0.1.18 sort wt0h1_v2/tmp/accepted_hits17.bam wt0h1_v2/tmp/accepted_hits17_sorted
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.Linux_x86_64/samtools_0.1.18 merge -f -h wt0h1_v2/tmp/genome_genome.bwt.samheader.sam wt0h1_v2/accepted_hits.bam wt0h1_v2/tmp/accepted_hits0_sorted.bam wt0h1_v2/tmp/accepted_hits1_sorted.bam wt0h1_v2/tmp/accepted_hits2_sorted.bam wt0h1_v2/tmp/accepted_hits3_sorted.bam wt0h1_v2/tmp/accepted_hits4_sorted.bam wt0h1_v2/tmp/accepted_hits5_sorted.bam wt0h1_v2/tmp/accepted_hits6_sorted.bam wt0h1_v2/tmp/accepted_hits7_sorted.bam wt0h1_v2/tmp/accepted_hits8_sorted.bam wt0h1_v2/tmp/accepted_hits9_sorted.bam wt0h1_v2/tmp/accepted_hits10_sorted.bam wt0h1_v2/tmp/accepted_hits11_sorted.bam wt0h1_v2/tmp/accepted_hits12_sorted.bam wt0h1_v2/tmp/accepted_hits13_sorted.bam wt0h1_v2/tmp/accepted_hits14_sorted.bam wt0h1_v2/tmp/accepted_hits15_sorted.bam wt0h1_v2/tmp/accepted_hits16_sorted.bam wt0h1_v2/tmp/accepted_hits17_sorted.bam
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.Linux_x86_64/bam_merge -Q --sam-header wt0h1_v2/tmp/genome_genome.bwt.samheader.sam wt0h1_v2/unmapped.bam wt0h1_v2/tmp/unmapped_left_0.bam wt0h1_v2/tmp/unmapped_right_0.bam wt0h1_v2/tmp/unmapped_left_1.bam wt0h1_v2/tmp/unmapped_right_1.bam wt0h1_v2/tmp/unmapped_left_2.bam wt0h1_v2/tmp/unmapped_right_2.bam wt0h1_v2/tmp/unmapped_left_3.bam wt0h1_v2/tmp/unmapped_right_3.bam wt0h1_v2/tmp/unmapped_left_4.bam wt0h1_v2/tmp/unmapped_right_4.bam wt0h1_v2/tmp/unmapped_left_5.bam wt0h1_v2/tmp/unmapped_right_5.bam wt0h1_v2/tmp/unmapped_left_6.bam wt0h1_v2/tmp/unmapped_right_6.bam wt0h1_v2/tmp/unmapped_left_7.bam wt0h1_v2/tmp/unmapped_right_7.bam wt0h1_v2/tmp/unmapped_left_8.bam wt0h1_v2/tmp/unmapped_right_8.bam wt0h1_v2/tmp/unmapped_left_9.bam wt0h1_v2/tmp/unmapped_right_9.bam wt0h1_v2/tmp/unmapped_left_10.bam wt0h1_v2/tmp/unmapped_right_10.bam wt0h1_v2/tmp/unmapped_left_11.bam wt0h1_v2/tmp/unmapped_right_11.bam wt0h1_v2/tmp/unmapped_left_12.bam wt0h1_v2/tmp/unmapped_right_12.bam wt0h1_v2/tmp/unmapped_left_13.bam wt0h1_v2/tmp/unmapped_right_13.bam wt0h1_v2/tmp/unmapped_left_14.bam wt0h1_v2/tmp/unmapped_right_14.bam wt0h1_v2/tmp/unmapped_left_15.bam wt0h1_v2/tmp/unmapped_right_15.bam wt0h1_v2/tmp/unmapped_left_16.bam wt0h1_v2/tmp/unmapped_right_16.bam wt0h1_v2/tmp/unmapped_left_17.bam wt0h1_v2/tmp/unmapped_right_17.bam
#>alldone: