/data/results/tools/align/tophat-2.0.10.Linux_x86_64/tophat -p 8 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3 --output-dir tophat_005 --keep-fasta-order --transcriptome-index=/data/results/reference/mmu/Mus_musculus/UCSC/mm9/mRNA/transcripts /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome R_2014_06_24_05_42_51_user_ION-72-ITlab_MSRNAseq_140624_ITR19_ITR23.ITR19.IonXpressRNA_005.fastq
/data/results/tools/align/tophat-2.0.10.Linux_x86_64/gtf_juncs /data/results/reference/mmu/Mus_musculus/UCSC/mm9/mRNA/transcripts.gff  > tophat_005/tmp/transcripts.juncs
#>prep_reads:
/data/results/tools/align/tophat-2.0.10.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 tophat_005/ --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 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --max-insertion-length 3 --max-deletion-length 3 -z gzip -p8 --gtf-annotations /data/results/reference/mmu/Mus_musculus/UCSC/mm9/mRNA/transcripts.gff --gtf-juncs tophat_005/tmp/transcripts.juncs --no-closure-search --no-coverage-search --no-microexon-search --aux-outfile=tophat_005/prep_reads.info --index-outfile=tophat_005/tmp/left_kept_reads.bam.index --sam-header=tophat_005/tmp/genome_genome.bwt.samheader.sam --outfile=tophat_005/tmp/left_kept_reads.bam R_2014_06_24_05_42_51_user_ION-72-ITlab_MSRNAseq_140624_ITR19_ITR23.ITR19.IonXpressRNA_005.fastq
#>map_start:
/data/results/tools/align/tophat-2.0.10.Linux_x86_64/bam2fastx --all tophat_005/tmp/left_kept_reads.bam|/data/results/tools/align/bowtie2-2.1.0/bowtie2-align -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,-20,0 -p 8 --sam-no-hd -x /data/results/reference/mmu/Mus_musculus/UCSC/mm9/mRNA/transcripts -|/data/results/tools/align/tophat-2.0.10.Linux_x86_64/fix_map_ordering --bowtie2-min-score 20 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --sam-header tophat_005/tmp/transcripts.bwt.samheader.sam - - tophat_005/tmp/left_kept_reads.m2g_um.bam | /data/results/tools/align/tophat-2.0.10.Linux_x86_64/map2gtf --sam-header tophat_005/tmp/genome_genome.bwt.samheader.sam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/mRNA/transcripts.fa.tlst - tophat_005/tmp/left_kept_reads.m2g.bam > tophat_005/logs/m2g_left_kept_reads.out
/data/results/tools/align/tophat-2.0.10.Linux_x86_64/bam2fastx --all tophat_005/tmp/left_kept_reads.m2g_um.bam|/data/results/tools/align/bowtie2-2.1.0/bowtie2-align -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,-20,0 -p 8 --sam-no-hd -x /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome -|/data/results/tools/align/tophat-2.0.10.Linux_x86_64/fix_map_ordering --bowtie2-min-score 20 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_005/tmp/left_kept_reads.m2g_um.mapped.bam.index --sam-header tophat_005/tmp/genome_genome.bwt.samheader.sam - tophat_005/tmp/left_kept_reads.m2g_um.mapped.bam tophat_005/tmp/left_kept_reads.m2g_um_unmapped.bam
#>map_segments:
gzip -cd< tophat_005/tmp/left_kept_reads.m2g_um_seg1.fq.z|/data/results/tools/align/bowtie2-2.1.0/bowtie2-align -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome -|/data/results/tools/align/tophat-2.0.10.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_005/tmp/left_kept_reads.m2g_um_seg1.bam.index --sam-header tophat_005/tmp/genome_genome.bwt.samheader.sam - tophat_005/tmp/left_kept_reads.m2g_um_seg1.bam tophat_005/tmp/left_kept_reads.m2g_um_seg1_unmapped.bam
gzip -cd< tophat_005/tmp/left_kept_reads.m2g_um_seg2.fq.z|/data/results/tools/align/bowtie2-2.1.0/bowtie2-align -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome -|/data/results/tools/align/tophat-2.0.10.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_005/tmp/left_kept_reads.m2g_um_seg2.bam.index --sam-header tophat_005/tmp/genome_genome.bwt.samheader.sam - tophat_005/tmp/left_kept_reads.m2g_um_seg2.bam tophat_005/tmp/left_kept_reads.m2g_um_seg2_unmapped.bam
gzip -cd< tophat_005/tmp/left_kept_reads.m2g_um_seg3.fq.z|/data/results/tools/align/bowtie2-2.1.0/bowtie2-align -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome -|/data/results/tools/align/tophat-2.0.10.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_005/tmp/left_kept_reads.m2g_um_seg3.bam.index --sam-header tophat_005/tmp/genome_genome.bwt.samheader.sam - tophat_005/tmp/left_kept_reads.m2g_um_seg3.bam tophat_005/tmp/left_kept_reads.m2g_um_seg3_unmapped.bam
gzip -cd< tophat_005/tmp/left_kept_reads.m2g_um_seg4.fq.z|/data/results/tools/align/bowtie2-2.1.0/bowtie2-align -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome -|/data/results/tools/align/tophat-2.0.10.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_005/tmp/left_kept_reads.m2g_um_seg4.bam.index --sam-header tophat_005/tmp/genome_genome.bwt.samheader.sam - tophat_005/tmp/left_kept_reads.m2g_um_seg4.bam tophat_005/tmp/left_kept_reads.m2g_um_seg4_unmapped.bam
gzip -cd< tophat_005/tmp/left_kept_reads.m2g_um_seg5.fq.z|/data/results/tools/align/bowtie2-2.1.0/bowtie2-align -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome -|/data/results/tools/align/tophat-2.0.10.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_005/tmp/left_kept_reads.m2g_um_seg5.bam.index --sam-header tophat_005/tmp/genome_genome.bwt.samheader.sam - tophat_005/tmp/left_kept_reads.m2g_um_seg5.bam tophat_005/tmp/left_kept_reads.m2g_um_seg5_unmapped.bam
gzip -cd< tophat_005/tmp/left_kept_reads.m2g_um_seg6.fq.z|/data/results/tools/align/bowtie2-2.1.0/bowtie2-align -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome -|/data/results/tools/align/tophat-2.0.10.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_005/tmp/left_kept_reads.m2g_um_seg6.bam.index --sam-header tophat_005/tmp/genome_genome.bwt.samheader.sam - tophat_005/tmp/left_kept_reads.m2g_um_seg6.bam tophat_005/tmp/left_kept_reads.m2g_um_seg6_unmapped.bam
gzip -cd< tophat_005/tmp/left_kept_reads.m2g_um_seg7.fq.z|/data/results/tools/align/bowtie2-2.1.0/bowtie2-align -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome -|/data/results/tools/align/tophat-2.0.10.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_005/tmp/left_kept_reads.m2g_um_seg7.bam.index --sam-header tophat_005/tmp/genome_genome.bwt.samheader.sam - tophat_005/tmp/left_kept_reads.m2g_um_seg7.bam tophat_005/tmp/left_kept_reads.m2g_um_seg7_unmapped.bam
gzip -cd< tophat_005/tmp/left_kept_reads.m2g_um_seg8.fq.z|/data/results/tools/align/bowtie2-2.1.0/bowtie2-align -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome -|/data/results/tools/align/tophat-2.0.10.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_005/tmp/left_kept_reads.m2g_um_seg8.bam.index --sam-header tophat_005/tmp/genome_genome.bwt.samheader.sam - tophat_005/tmp/left_kept_reads.m2g_um_seg8.bam tophat_005/tmp/left_kept_reads.m2g_um_seg8_unmapped.bam
gzip -cd< tophat_005/tmp/left_kept_reads.m2g_um_seg9.fq.z|/data/results/tools/align/bowtie2-2.1.0/bowtie2-align -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome -|/data/results/tools/align/tophat-2.0.10.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_005/tmp/left_kept_reads.m2g_um_seg9.bam.index --sam-header tophat_005/tmp/genome_genome.bwt.samheader.sam - tophat_005/tmp/left_kept_reads.m2g_um_seg9.bam tophat_005/tmp/left_kept_reads.m2g_um_seg9_unmapped.bam
gzip -cd< tophat_005/tmp/left_kept_reads.m2g_um_seg10.fq.z|/data/results/tools/align/bowtie2-2.1.0/bowtie2-align -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome -|/data/results/tools/align/tophat-2.0.10.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_005/tmp/left_kept_reads.m2g_um_seg10.bam.index --sam-header tophat_005/tmp/genome_genome.bwt.samheader.sam - tophat_005/tmp/left_kept_reads.m2g_um_seg10.bam tophat_005/tmp/left_kept_reads.m2g_um_seg10_unmapped.bam
gzip -cd< tophat_005/tmp/left_kept_reads.m2g_um_seg11.fq.z|/data/results/tools/align/bowtie2-2.1.0/bowtie2-align -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome -|/data/results/tools/align/tophat-2.0.10.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_005/tmp/left_kept_reads.m2g_um_seg11.bam.index --sam-header tophat_005/tmp/genome_genome.bwt.samheader.sam - tophat_005/tmp/left_kept_reads.m2g_um_seg11.bam tophat_005/tmp/left_kept_reads.m2g_um_seg11_unmapped.bam
gzip -cd< tophat_005/tmp/left_kept_reads.m2g_um_seg12.fq.z|/data/results/tools/align/bowtie2-2.1.0/bowtie2-align -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome -|/data/results/tools/align/tophat-2.0.10.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_005/tmp/left_kept_reads.m2g_um_seg12.bam.index --sam-header tophat_005/tmp/genome_genome.bwt.samheader.sam - tophat_005/tmp/left_kept_reads.m2g_um_seg12.bam tophat_005/tmp/left_kept_reads.m2g_um_seg12_unmapped.bam
gzip -cd< tophat_005/tmp/left_kept_reads.m2g_um_seg13.fq.z|/data/results/tools/align/bowtie2-2.1.0/bowtie2-align -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome -|/data/results/tools/align/tophat-2.0.10.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_005/tmp/left_kept_reads.m2g_um_seg13.bam.index --sam-header tophat_005/tmp/genome_genome.bwt.samheader.sam - tophat_005/tmp/left_kept_reads.m2g_um_seg13.bam tophat_005/tmp/left_kept_reads.m2g_um_seg13_unmapped.bam
gzip -cd< tophat_005/tmp/left_kept_reads.m2g_um_seg14.fq.z|/data/results/tools/align/bowtie2-2.1.0/bowtie2-align -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome -|/data/results/tools/align/tophat-2.0.10.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_005/tmp/left_kept_reads.m2g_um_seg14.bam.index --sam-header tophat_005/tmp/genome_genome.bwt.samheader.sam - tophat_005/tmp/left_kept_reads.m2g_um_seg14.bam tophat_005/tmp/left_kept_reads.m2g_um_seg14_unmapped.bam
gzip -cd< tophat_005/tmp/left_kept_reads.m2g_um_seg15.fq.z|/data/results/tools/align/bowtie2-2.1.0/bowtie2-align -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome -|/data/results/tools/align/tophat-2.0.10.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_005/tmp/left_kept_reads.m2g_um_seg15.bam.index --sam-header tophat_005/tmp/genome_genome.bwt.samheader.sam - tophat_005/tmp/left_kept_reads.m2g_um_seg15.bam tophat_005/tmp/left_kept_reads.m2g_um_seg15_unmapped.bam
#>find_juncs:
/data/results/tools/align/tophat-2.0.10.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 tophat_005/ --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 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --max-insertion-length 3 --max-deletion-length 3 -z gzip -p8 --gtf-annotations /data/results/reference/mmu/Mus_musculus/UCSC/mm9/mRNA/transcripts.gff --gtf-juncs tophat_005/tmp/transcripts.juncs --no-closure-search --no-coverage-search --no-microexon-search --sam-header tophat_005/tmp/genome_genome.bwt.samheader.sam --ium-reads tophat_005/tmp/left_kept_reads.m2g_um_seg1_unmapped.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg2_unmapped.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg3_unmapped.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg4_unmapped.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg5_unmapped.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg6_unmapped.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg7_unmapped.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg8_unmapped.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg9_unmapped.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg10_unmapped.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg11_unmapped.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg12_unmapped.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg13_unmapped.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg14_unmapped.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg15_unmapped.bam /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome.fa tophat_005/tmp/segment.juncs tophat_005/tmp/segment.insertions tophat_005/tmp/segment.deletions tophat_005/tmp/segment.fusions tophat_005/tmp/left_kept_reads.bam tophat_005/tmp/left_kept_reads.m2g_um.mapped.bam tophat_005/tmp/left_kept_reads.m2g_um_seg1.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg2.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg3.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg4.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg5.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg6.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg7.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg8.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg9.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg10.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg11.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg12.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg13.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg14.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg15.bam
#>juncs_db:
/data/results/tools/align/tophat-2.0.10.Linux_x86_64/juncs_db 3 25 tophat_005/tmp/transcripts.juncs,tophat_005/tmp/segment.juncs /dev/null /dev/null /dev/null /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome.fa > tophat_005/tmp/segment_juncs.fa
/data/results/tools/align/bowtie2-2.1.0/bowtie2-build tophat_005/tmp/segment_juncs.fa tophat_005/tmp/segment_juncs
#>map2juncs:
gzip -cd< tophat_005/tmp/left_kept_reads.m2g_um_seg1.fq.z|/data/results/tools/align/bowtie2-2.1.0/bowtie2-align -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x tophat_005/tmp/segment_juncs -|/data/results/tools/align/tophat-2.0.10.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_005/tmp/left_kept_reads.m2g_um_seg1.to_spliced.bam.index --sam-header tophat_005/tmp/segment_juncs.bwt.samheader.sam - tophat_005/tmp/left_kept_reads.m2g_um_seg1.to_spliced.bam
gzip -cd< tophat_005/tmp/left_kept_reads.m2g_um_seg2.fq.z|/data/results/tools/align/bowtie2-2.1.0/bowtie2-align -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x tophat_005/tmp/segment_juncs -|/data/results/tools/align/tophat-2.0.10.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_005/tmp/left_kept_reads.m2g_um_seg2.to_spliced.bam.index --sam-header tophat_005/tmp/segment_juncs.bwt.samheader.sam - tophat_005/tmp/left_kept_reads.m2g_um_seg2.to_spliced.bam
gzip -cd< tophat_005/tmp/left_kept_reads.m2g_um_seg3.fq.z|/data/results/tools/align/bowtie2-2.1.0/bowtie2-align -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x tophat_005/tmp/segment_juncs -|/data/results/tools/align/tophat-2.0.10.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_005/tmp/left_kept_reads.m2g_um_seg3.to_spliced.bam.index --sam-header tophat_005/tmp/segment_juncs.bwt.samheader.sam - tophat_005/tmp/left_kept_reads.m2g_um_seg3.to_spliced.bam
gzip -cd< tophat_005/tmp/left_kept_reads.m2g_um_seg4.fq.z|/data/results/tools/align/bowtie2-2.1.0/bowtie2-align -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x tophat_005/tmp/segment_juncs -|/data/results/tools/align/tophat-2.0.10.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_005/tmp/left_kept_reads.m2g_um_seg4.to_spliced.bam.index --sam-header tophat_005/tmp/segment_juncs.bwt.samheader.sam - tophat_005/tmp/left_kept_reads.m2g_um_seg4.to_spliced.bam
gzip -cd< tophat_005/tmp/left_kept_reads.m2g_um_seg5.fq.z|/data/results/tools/align/bowtie2-2.1.0/bowtie2-align -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x tophat_005/tmp/segment_juncs -|/data/results/tools/align/tophat-2.0.10.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_005/tmp/left_kept_reads.m2g_um_seg5.to_spliced.bam.index --sam-header tophat_005/tmp/segment_juncs.bwt.samheader.sam - tophat_005/tmp/left_kept_reads.m2g_um_seg5.to_spliced.bam
gzip -cd< tophat_005/tmp/left_kept_reads.m2g_um_seg6.fq.z|/data/results/tools/align/bowtie2-2.1.0/bowtie2-align -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x tophat_005/tmp/segment_juncs -|/data/results/tools/align/tophat-2.0.10.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_005/tmp/left_kept_reads.m2g_um_seg6.to_spliced.bam.index --sam-header tophat_005/tmp/segment_juncs.bwt.samheader.sam - tophat_005/tmp/left_kept_reads.m2g_um_seg6.to_spliced.bam
gzip -cd< tophat_005/tmp/left_kept_reads.m2g_um_seg7.fq.z|/data/results/tools/align/bowtie2-2.1.0/bowtie2-align -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x tophat_005/tmp/segment_juncs -|/data/results/tools/align/tophat-2.0.10.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_005/tmp/left_kept_reads.m2g_um_seg7.to_spliced.bam.index --sam-header tophat_005/tmp/segment_juncs.bwt.samheader.sam - tophat_005/tmp/left_kept_reads.m2g_um_seg7.to_spliced.bam
gzip -cd< tophat_005/tmp/left_kept_reads.m2g_um_seg8.fq.z|/data/results/tools/align/bowtie2-2.1.0/bowtie2-align -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x tophat_005/tmp/segment_juncs -|/data/results/tools/align/tophat-2.0.10.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_005/tmp/left_kept_reads.m2g_um_seg8.to_spliced.bam.index --sam-header tophat_005/tmp/segment_juncs.bwt.samheader.sam - tophat_005/tmp/left_kept_reads.m2g_um_seg8.to_spliced.bam
gzip -cd< tophat_005/tmp/left_kept_reads.m2g_um_seg9.fq.z|/data/results/tools/align/bowtie2-2.1.0/bowtie2-align -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x tophat_005/tmp/segment_juncs -|/data/results/tools/align/tophat-2.0.10.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_005/tmp/left_kept_reads.m2g_um_seg9.to_spliced.bam.index --sam-header tophat_005/tmp/segment_juncs.bwt.samheader.sam - tophat_005/tmp/left_kept_reads.m2g_um_seg9.to_spliced.bam
gzip -cd< tophat_005/tmp/left_kept_reads.m2g_um_seg10.fq.z|/data/results/tools/align/bowtie2-2.1.0/bowtie2-align -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x tophat_005/tmp/segment_juncs -|/data/results/tools/align/tophat-2.0.10.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_005/tmp/left_kept_reads.m2g_um_seg10.to_spliced.bam.index --sam-header tophat_005/tmp/segment_juncs.bwt.samheader.sam - tophat_005/tmp/left_kept_reads.m2g_um_seg10.to_spliced.bam
gzip -cd< tophat_005/tmp/left_kept_reads.m2g_um_seg11.fq.z|/data/results/tools/align/bowtie2-2.1.0/bowtie2-align -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x tophat_005/tmp/segment_juncs -|/data/results/tools/align/tophat-2.0.10.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_005/tmp/left_kept_reads.m2g_um_seg11.to_spliced.bam.index --sam-header tophat_005/tmp/segment_juncs.bwt.samheader.sam - tophat_005/tmp/left_kept_reads.m2g_um_seg11.to_spliced.bam
gzip -cd< tophat_005/tmp/left_kept_reads.m2g_um_seg12.fq.z|/data/results/tools/align/bowtie2-2.1.0/bowtie2-align -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x tophat_005/tmp/segment_juncs -|/data/results/tools/align/tophat-2.0.10.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_005/tmp/left_kept_reads.m2g_um_seg12.to_spliced.bam.index --sam-header tophat_005/tmp/segment_juncs.bwt.samheader.sam - tophat_005/tmp/left_kept_reads.m2g_um_seg12.to_spliced.bam
gzip -cd< tophat_005/tmp/left_kept_reads.m2g_um_seg13.fq.z|/data/results/tools/align/bowtie2-2.1.0/bowtie2-align -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x tophat_005/tmp/segment_juncs -|/data/results/tools/align/tophat-2.0.10.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_005/tmp/left_kept_reads.m2g_um_seg13.to_spliced.bam.index --sam-header tophat_005/tmp/segment_juncs.bwt.samheader.sam - tophat_005/tmp/left_kept_reads.m2g_um_seg13.to_spliced.bam
gzip -cd< tophat_005/tmp/left_kept_reads.m2g_um_seg14.fq.z|/data/results/tools/align/bowtie2-2.1.0/bowtie2-align -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x tophat_005/tmp/segment_juncs -|/data/results/tools/align/tophat-2.0.10.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_005/tmp/left_kept_reads.m2g_um_seg14.to_spliced.bam.index --sam-header tophat_005/tmp/segment_juncs.bwt.samheader.sam - tophat_005/tmp/left_kept_reads.m2g_um_seg14.to_spliced.bam
gzip -cd< tophat_005/tmp/left_kept_reads.m2g_um_seg15.fq.z|/data/results/tools/align/bowtie2-2.1.0/bowtie2-align -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x tophat_005/tmp/segment_juncs -|/data/results/tools/align/tophat-2.0.10.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_005/tmp/left_kept_reads.m2g_um_seg15.to_spliced.bam.index --sam-header tophat_005/tmp/segment_juncs.bwt.samheader.sam - tophat_005/tmp/left_kept_reads.m2g_um_seg15.to_spliced.bam
/data/results/tools/align/tophat-2.0.10.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 tophat_005/ --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 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --max-insertion-length 3 --max-deletion-length 3 -z gzip -p8 --gtf-annotations /data/results/reference/mmu/Mus_musculus/UCSC/mm9/mRNA/transcripts.gff --gtf-juncs tophat_005/tmp/transcripts.juncs --no-closure-search --no-coverage-search --no-microexon-search --sam-header tophat_005/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 tophat_005/tmp/left_kept_reads.m2g_um.bam tophat_005/tmp/transcripts.juncs,tophat_005/tmp/segment.juncs tophat_005/tmp/segment.insertions tophat_005/tmp/segment.deletions /dev/null tophat_005/tmp/left_kept_reads.m2g_um.candidates.bam tophat_005/tmp/left_kept_reads.m2g_um_seg1.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg2.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg3.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg4.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg5.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg6.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg7.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg8.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg9.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg10.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg11.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg12.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg13.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg14.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg15.bam tophat_005/tmp/left_kept_reads.m2g_um_seg1.to_spliced.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg2.to_spliced.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg3.to_spliced.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg4.to_spliced.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg5.to_spliced.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg6.to_spliced.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg7.to_spliced.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg8.to_spliced.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg9.to_spliced.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg10.to_spliced.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg11.to_spliced.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg12.to_spliced.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg13.to_spliced.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg14.to_spliced.bam,tophat_005/tmp/left_kept_reads.m2g_um_seg15.to_spliced.bam
#>tophat_reports:
/data/results/tools/align/tophat-2.0.10.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 tophat_005/ --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 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --max-insertion-length 3 --max-deletion-length 3 -z gzip -p8 --gtf-annotations /data/results/reference/mmu/Mus_musculus/UCSC/mm9/mRNA/transcripts.gff --gtf-juncs tophat_005/tmp/transcripts.juncs --no-closure-search --no-coverage-search --no-microexon-search --sam-header tophat_005/tmp/genome_genome.bwt.samheader.sam --report-discordant-pair-alignments --report-mixed-alignments --samtools=/usr/bin/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 /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome.fa tophat_005/junctions.bed tophat_005/insertions.bed tophat_005/deletions.bed tophat_005/fusions.out tophat_005/tmp/accepted_hits tophat_005/tmp/left_kept_reads.m2g.bam,tophat_005/tmp/left_kept_reads.m2g_um.mapped.bam,tophat_005/tmp/left_kept_reads.m2g_um.candidates.bam tophat_005/tmp/left_kept_reads.bam
/usr/bin/samtools sort tophat_005/tmp/accepted_hits0.bam tophat_005/tmp/accepted_hits0_sorted
/usr/bin/samtools sort tophat_005/tmp/accepted_hits1.bam tophat_005/tmp/accepted_hits1_sorted
/usr/bin/samtools sort tophat_005/tmp/accepted_hits2.bam tophat_005/tmp/accepted_hits2_sorted
/usr/bin/samtools sort tophat_005/tmp/accepted_hits3.bam tophat_005/tmp/accepted_hits3_sorted
/usr/bin/samtools sort tophat_005/tmp/accepted_hits4.bam tophat_005/tmp/accepted_hits4_sorted
/usr/bin/samtools sort tophat_005/tmp/accepted_hits5.bam tophat_005/tmp/accepted_hits5_sorted
/usr/bin/samtools sort tophat_005/tmp/accepted_hits6.bam tophat_005/tmp/accepted_hits6_sorted
/usr/bin/samtools sort tophat_005/tmp/accepted_hits7.bam tophat_005/tmp/accepted_hits7_sorted
/usr/bin/samtools merge -f -h tophat_005/tmp/genome_genome.bwt.samheader.sam tophat_005/accepted_hits.bam tophat_005/tmp/accepted_hits0_sorted.bam tophat_005/tmp/accepted_hits1_sorted.bam tophat_005/tmp/accepted_hits2_sorted.bam tophat_005/tmp/accepted_hits3_sorted.bam tophat_005/tmp/accepted_hits4_sorted.bam tophat_005/tmp/accepted_hits5_sorted.bam tophat_005/tmp/accepted_hits6_sorted.bam tophat_005/tmp/accepted_hits7_sorted.bam
/data/results/tools/align/tophat-2.0.10.Linux_x86_64/bam_merge -Q --sam-header tophat_005/tmp/genome_genome.bwt.samheader.sam tophat_005/unmapped.bam tophat_005/tmp/unmapped_left_0.bam tophat_005/tmp/unmapped_left_1.bam tophat_005/tmp/unmapped_left_2.bam tophat_005/tmp/unmapped_left_3.bam tophat_005/tmp/unmapped_left_4.bam tophat_005/tmp/unmapped_left_5.bam tophat_005/tmp/unmapped_left_6.bam tophat_005/tmp/unmapped_left_7.bam
#>alldone: