/data/results/tools/align/tophat-2.1.1.Linux_x86_64/tophat -p 4 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3 --no-novel-juncs --output-dir tophat_010 --keep-fasta-order --transcriptome-index=/data/results/reference/mmu/mm10/mRNA/transcripts --GTF /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Annotation/Archives/archive-2015-07-17-14-33-26/Genes/genes.gtf /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/genome R_2021_02_10_13_23_39_user_IONAS-464-MD-EDlabs_210210_ED3R9-11_MD3R17-31.ED3R10_993.IonXpress_010.fastq
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.Linux_x86_64/gtf_juncs /data/results/reference/mmu/mm10/mRNA/transcripts.gff  > tophat_010/tmp/transcripts.juncs
#>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 tophat_010/ --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 -p4 --gtf-annotations /data/results/reference/mmu/mm10/mRNA/transcripts.gff --gtf-juncs tophat_010/tmp/transcripts.juncs --no-closure-search --no-coverage-search --no-microexon-search --aux-outfile=tophat_010/prep_reads.info --index-outfile=tophat_010/tmp/left_kept_reads.bam.index --sam-header=tophat_010/tmp/genome_genome.bwt.samheader.sam --outfile=tophat_010/tmp/left_kept_reads.bam R_2021_02_10_13_23_39_user_IONAS-464-MD-EDlabs_210210_ED3R9-11_MD3R17-31.ED3R10_993.IonXpress_010.fastq
#>map_start:
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.Linux_x86_64/bam2fastx --all tophat_010/tmp/left_kept_reads.bam|/data/results/tools/align/bowtie2-2.2.8/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,-20,0 -p 4 --sam-no-hd -x /data/results/reference/mmu/mm10/mRNA/transcripts -|/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.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_010/tmp/transcripts.bwt.samheader.sam - - tophat_010/tmp/left_kept_reads.m2g_um.bam | /mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.Linux_x86_64/map2gtf --sam-header tophat_010/tmp/genome_genome.bwt.samheader.sam /data/results/reference/mmu/mm10/mRNA/transcripts.fa.tlst - tophat_010/tmp/left_kept_reads.m2g.bam > tophat_010/logs/m2g_left_kept_reads.out
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.Linux_x86_64/bam2fastx --all tophat_010/tmp/left_kept_reads.m2g_um.bam|/data/results/tools/align/bowtie2-2.2.8/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,-20,0 -p 4 --sam-no-hd -x /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/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 20 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_010/tmp/left_kept_reads.m2g_um.mapped.bam.index --sam-header tophat_010/tmp/genome_genome.bwt.samheader.sam - tophat_010/tmp/left_kept_reads.m2g_um.mapped.bam tophat_010/tmp/left_kept_reads.m2g_um_unmapped.bam
#>map_segments:
gzip -cd< tophat_010/tmp/left_kept_reads.m2g_um_seg1.fq.z|/data/results/tools/align/bowtie2-2.2.8/bowtie2 -k 41 -N 1 -L 20 -p 4 --sam-no-hd -x /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/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 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_010/tmp/left_kept_reads.m2g_um_seg1.bam.index --sam-header tophat_010/tmp/genome_genome.bwt.samheader.sam - tophat_010/tmp/left_kept_reads.m2g_um_seg1.bam tophat_010/tmp/left_kept_reads.m2g_um_seg1_unmapped.bam
gzip -cd< tophat_010/tmp/left_kept_reads.m2g_um_seg2.fq.z|/data/results/tools/align/bowtie2-2.2.8/bowtie2 -k 41 -N 1 -L 20 -p 4 --sam-no-hd -x /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/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 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_010/tmp/left_kept_reads.m2g_um_seg2.bam.index --sam-header tophat_010/tmp/genome_genome.bwt.samheader.sam - tophat_010/tmp/left_kept_reads.m2g_um_seg2.bam tophat_010/tmp/left_kept_reads.m2g_um_seg2_unmapped.bam
gzip -cd< tophat_010/tmp/left_kept_reads.m2g_um_seg3.fq.z|/data/results/tools/align/bowtie2-2.2.8/bowtie2 -k 41 -N 1 -L 20 -p 4 --sam-no-hd -x /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/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 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_010/tmp/left_kept_reads.m2g_um_seg3.bam.index --sam-header tophat_010/tmp/genome_genome.bwt.samheader.sam - tophat_010/tmp/left_kept_reads.m2g_um_seg3.bam tophat_010/tmp/left_kept_reads.m2g_um_seg3_unmapped.bam
gzip -cd< tophat_010/tmp/left_kept_reads.m2g_um_seg4.fq.z|/data/results/tools/align/bowtie2-2.2.8/bowtie2 -k 41 -N 1 -L 20 -p 4 --sam-no-hd -x /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/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 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_010/tmp/left_kept_reads.m2g_um_seg4.bam.index --sam-header tophat_010/tmp/genome_genome.bwt.samheader.sam - tophat_010/tmp/left_kept_reads.m2g_um_seg4.bam tophat_010/tmp/left_kept_reads.m2g_um_seg4_unmapped.bam
gzip -cd< tophat_010/tmp/left_kept_reads.m2g_um_seg5.fq.z|/data/results/tools/align/bowtie2-2.2.8/bowtie2 -k 41 -N 1 -L 20 -p 4 --sam-no-hd -x /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/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 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_010/tmp/left_kept_reads.m2g_um_seg5.bam.index --sam-header tophat_010/tmp/genome_genome.bwt.samheader.sam - tophat_010/tmp/left_kept_reads.m2g_um_seg5.bam tophat_010/tmp/left_kept_reads.m2g_um_seg5_unmapped.bam
gzip -cd< tophat_010/tmp/left_kept_reads.m2g_um_seg6.fq.z|/data/results/tools/align/bowtie2-2.2.8/bowtie2 -k 41 -N 1 -L 20 -p 4 --sam-no-hd -x /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/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 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_010/tmp/left_kept_reads.m2g_um_seg6.bam.index --sam-header tophat_010/tmp/genome_genome.bwt.samheader.sam - tophat_010/tmp/left_kept_reads.m2g_um_seg6.bam tophat_010/tmp/left_kept_reads.m2g_um_seg6_unmapped.bam
gzip -cd< tophat_010/tmp/left_kept_reads.m2g_um_seg7.fq.z|/data/results/tools/align/bowtie2-2.2.8/bowtie2 -k 41 -N 1 -L 20 -p 4 --sam-no-hd -x /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/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 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_010/tmp/left_kept_reads.m2g_um_seg7.bam.index --sam-header tophat_010/tmp/genome_genome.bwt.samheader.sam - tophat_010/tmp/left_kept_reads.m2g_um_seg7.bam tophat_010/tmp/left_kept_reads.m2g_um_seg7_unmapped.bam
gzip -cd< tophat_010/tmp/left_kept_reads.m2g_um_seg8.fq.z|/data/results/tools/align/bowtie2-2.2.8/bowtie2 -k 41 -N 1 -L 20 -p 4 --sam-no-hd -x /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/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 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_010/tmp/left_kept_reads.m2g_um_seg8.bam.index --sam-header tophat_010/tmp/genome_genome.bwt.samheader.sam - tophat_010/tmp/left_kept_reads.m2g_um_seg8.bam tophat_010/tmp/left_kept_reads.m2g_um_seg8_unmapped.bam
gzip -cd< tophat_010/tmp/left_kept_reads.m2g_um_seg9.fq.z|/data/results/tools/align/bowtie2-2.2.8/bowtie2 -k 41 -N 1 -L 20 -p 4 --sam-no-hd -x /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/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 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_010/tmp/left_kept_reads.m2g_um_seg9.bam.index --sam-header tophat_010/tmp/genome_genome.bwt.samheader.sam - tophat_010/tmp/left_kept_reads.m2g_um_seg9.bam tophat_010/tmp/left_kept_reads.m2g_um_seg9_unmapped.bam
gzip -cd< tophat_010/tmp/left_kept_reads.m2g_um_seg10.fq.z|/data/results/tools/align/bowtie2-2.2.8/bowtie2 -k 41 -N 1 -L 20 -p 4 --sam-no-hd -x /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/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 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_010/tmp/left_kept_reads.m2g_um_seg10.bam.index --sam-header tophat_010/tmp/genome_genome.bwt.samheader.sam - tophat_010/tmp/left_kept_reads.m2g_um_seg10.bam tophat_010/tmp/left_kept_reads.m2g_um_seg10_unmapped.bam
gzip -cd< tophat_010/tmp/left_kept_reads.m2g_um_seg11.fq.z|/data/results/tools/align/bowtie2-2.2.8/bowtie2 -k 41 -N 1 -L 20 -p 4 --sam-no-hd -x /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/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 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_010/tmp/left_kept_reads.m2g_um_seg11.bam.index --sam-header tophat_010/tmp/genome_genome.bwt.samheader.sam - tophat_010/tmp/left_kept_reads.m2g_um_seg11.bam tophat_010/tmp/left_kept_reads.m2g_um_seg11_unmapped.bam
gzip -cd< tophat_010/tmp/left_kept_reads.m2g_um_seg12.fq.z|/data/results/tools/align/bowtie2-2.2.8/bowtie2 -k 41 -N 1 -L 20 -p 4 --sam-no-hd -x /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/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 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_010/tmp/left_kept_reads.m2g_um_seg12.bam.index --sam-header tophat_010/tmp/genome_genome.bwt.samheader.sam - tophat_010/tmp/left_kept_reads.m2g_um_seg12.bam tophat_010/tmp/left_kept_reads.m2g_um_seg12_unmapped.bam
gzip -cd< tophat_010/tmp/left_kept_reads.m2g_um_seg13.fq.z|/data/results/tools/align/bowtie2-2.2.8/bowtie2 -k 41 -N 1 -L 20 -p 4 --sam-no-hd -x /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/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 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_010/tmp/left_kept_reads.m2g_um_seg13.bam.index --sam-header tophat_010/tmp/genome_genome.bwt.samheader.sam - tophat_010/tmp/left_kept_reads.m2g_um_seg13.bam tophat_010/tmp/left_kept_reads.m2g_um_seg13_unmapped.bam
gzip -cd< tophat_010/tmp/left_kept_reads.m2g_um_seg14.fq.z|/data/results/tools/align/bowtie2-2.2.8/bowtie2 -k 41 -N 1 -L 20 -p 4 --sam-no-hd -x /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/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 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_010/tmp/left_kept_reads.m2g_um_seg14.bam.index --sam-header tophat_010/tmp/genome_genome.bwt.samheader.sam - tophat_010/tmp/left_kept_reads.m2g_um_seg14.bam tophat_010/tmp/left_kept_reads.m2g_um_seg14_unmapped.bam
#>juncs_db:
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.Linux_x86_64/juncs_db 3 36 tophat_010/tmp/transcripts.juncs /dev/null /dev/null /dev/null /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/genome.fa > tophat_010/tmp/segment_juncs.fa
/data/results/tools/align/bowtie2-2.2.8/bowtie2-build tophat_010/tmp/segment_juncs.fa tophat_010/tmp/segment_juncs
#>map2juncs:
gzip -cd< tophat_010/tmp/left_kept_reads.m2g_um_seg1.fq.z|/data/results/tools/align/bowtie2-2.2.8/bowtie2 -k 41 -N 1 -L 20 -p 4 --sam-no-hd -x tophat_010/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 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_010/tmp/left_kept_reads.m2g_um_seg1.to_spliced.bam.index --sam-header tophat_010/tmp/segment_juncs.bwt.samheader.sam - tophat_010/tmp/left_kept_reads.m2g_um_seg1.to_spliced.bam
gzip -cd< tophat_010/tmp/left_kept_reads.m2g_um_seg2.fq.z|/data/results/tools/align/bowtie2-2.2.8/bowtie2 -k 41 -N 1 -L 20 -p 4 --sam-no-hd -x tophat_010/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 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_010/tmp/left_kept_reads.m2g_um_seg2.to_spliced.bam.index --sam-header tophat_010/tmp/segment_juncs.bwt.samheader.sam - tophat_010/tmp/left_kept_reads.m2g_um_seg2.to_spliced.bam
gzip -cd< tophat_010/tmp/left_kept_reads.m2g_um_seg3.fq.z|/data/results/tools/align/bowtie2-2.2.8/bowtie2 -k 41 -N 1 -L 20 -p 4 --sam-no-hd -x tophat_010/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 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_010/tmp/left_kept_reads.m2g_um_seg3.to_spliced.bam.index --sam-header tophat_010/tmp/segment_juncs.bwt.samheader.sam - tophat_010/tmp/left_kept_reads.m2g_um_seg3.to_spliced.bam
gzip -cd< tophat_010/tmp/left_kept_reads.m2g_um_seg4.fq.z|/data/results/tools/align/bowtie2-2.2.8/bowtie2 -k 41 -N 1 -L 20 -p 4 --sam-no-hd -x tophat_010/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 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_010/tmp/left_kept_reads.m2g_um_seg4.to_spliced.bam.index --sam-header tophat_010/tmp/segment_juncs.bwt.samheader.sam - tophat_010/tmp/left_kept_reads.m2g_um_seg4.to_spliced.bam
gzip -cd< tophat_010/tmp/left_kept_reads.m2g_um_seg5.fq.z|/data/results/tools/align/bowtie2-2.2.8/bowtie2 -k 41 -N 1 -L 20 -p 4 --sam-no-hd -x tophat_010/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 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_010/tmp/left_kept_reads.m2g_um_seg5.to_spliced.bam.index --sam-header tophat_010/tmp/segment_juncs.bwt.samheader.sam - tophat_010/tmp/left_kept_reads.m2g_um_seg5.to_spliced.bam
gzip -cd< tophat_010/tmp/left_kept_reads.m2g_um_seg6.fq.z|/data/results/tools/align/bowtie2-2.2.8/bowtie2 -k 41 -N 1 -L 20 -p 4 --sam-no-hd -x tophat_010/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 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_010/tmp/left_kept_reads.m2g_um_seg6.to_spliced.bam.index --sam-header tophat_010/tmp/segment_juncs.bwt.samheader.sam - tophat_010/tmp/left_kept_reads.m2g_um_seg6.to_spliced.bam
gzip -cd< tophat_010/tmp/left_kept_reads.m2g_um_seg7.fq.z|/data/results/tools/align/bowtie2-2.2.8/bowtie2 -k 41 -N 1 -L 20 -p 4 --sam-no-hd -x tophat_010/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 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_010/tmp/left_kept_reads.m2g_um_seg7.to_spliced.bam.index --sam-header tophat_010/tmp/segment_juncs.bwt.samheader.sam - tophat_010/tmp/left_kept_reads.m2g_um_seg7.to_spliced.bam
gzip -cd< tophat_010/tmp/left_kept_reads.m2g_um_seg8.fq.z|/data/results/tools/align/bowtie2-2.2.8/bowtie2 -k 41 -N 1 -L 20 -p 4 --sam-no-hd -x tophat_010/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 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_010/tmp/left_kept_reads.m2g_um_seg8.to_spliced.bam.index --sam-header tophat_010/tmp/segment_juncs.bwt.samheader.sam - tophat_010/tmp/left_kept_reads.m2g_um_seg8.to_spliced.bam
gzip -cd< tophat_010/tmp/left_kept_reads.m2g_um_seg9.fq.z|/data/results/tools/align/bowtie2-2.2.8/bowtie2 -k 41 -N 1 -L 20 -p 4 --sam-no-hd -x tophat_010/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 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_010/tmp/left_kept_reads.m2g_um_seg9.to_spliced.bam.index --sam-header tophat_010/tmp/segment_juncs.bwt.samheader.sam - tophat_010/tmp/left_kept_reads.m2g_um_seg9.to_spliced.bam
gzip -cd< tophat_010/tmp/left_kept_reads.m2g_um_seg10.fq.z|/data/results/tools/align/bowtie2-2.2.8/bowtie2 -k 41 -N 1 -L 20 -p 4 --sam-no-hd -x tophat_010/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 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_010/tmp/left_kept_reads.m2g_um_seg10.to_spliced.bam.index --sam-header tophat_010/tmp/segment_juncs.bwt.samheader.sam - tophat_010/tmp/left_kept_reads.m2g_um_seg10.to_spliced.bam
gzip -cd< tophat_010/tmp/left_kept_reads.m2g_um_seg11.fq.z|/data/results/tools/align/bowtie2-2.2.8/bowtie2 -k 41 -N 1 -L 20 -p 4 --sam-no-hd -x tophat_010/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 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_010/tmp/left_kept_reads.m2g_um_seg11.to_spliced.bam.index --sam-header tophat_010/tmp/segment_juncs.bwt.samheader.sam - tophat_010/tmp/left_kept_reads.m2g_um_seg11.to_spliced.bam
gzip -cd< tophat_010/tmp/left_kept_reads.m2g_um_seg12.fq.z|/data/results/tools/align/bowtie2-2.2.8/bowtie2 -k 41 -N 1 -L 20 -p 4 --sam-no-hd -x tophat_010/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 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_010/tmp/left_kept_reads.m2g_um_seg12.to_spliced.bam.index --sam-header tophat_010/tmp/segment_juncs.bwt.samheader.sam - tophat_010/tmp/left_kept_reads.m2g_um_seg12.to_spliced.bam
gzip -cd< tophat_010/tmp/left_kept_reads.m2g_um_seg13.fq.z|/data/results/tools/align/bowtie2-2.2.8/bowtie2 -k 41 -N 1 -L 20 -p 4 --sam-no-hd -x tophat_010/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 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_010/tmp/left_kept_reads.m2g_um_seg13.to_spliced.bam.index --sam-header tophat_010/tmp/segment_juncs.bwt.samheader.sam - tophat_010/tmp/left_kept_reads.m2g_um_seg13.to_spliced.bam
gzip -cd< tophat_010/tmp/left_kept_reads.m2g_um_seg14.fq.z|/data/results/tools/align/bowtie2-2.2.8/bowtie2 -k 41 -N 1 -L 20 -p 4 --sam-no-hd -x tophat_010/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 3 --read-gap-length 3 --read-edit-dist 3 --read-realign-edit-dist 4 --index-outfile tophat_010/tmp/left_kept_reads.m2g_um_seg14.to_spliced.bam.index --sam-header tophat_010/tmp/segment_juncs.bwt.samheader.sam - tophat_010/tmp/left_kept_reads.m2g_um_seg14.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 tophat_010/ --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 -p4 --gtf-annotations /data/results/reference/mmu/mm10/mRNA/transcripts.gff --gtf-juncs tophat_010/tmp/transcripts.juncs --no-closure-search --no-coverage-search --no-microexon-search --sam-header tophat_010/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/mm10/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/genome.fa tophat_010/tmp/left_kept_reads.m2g_um.bam tophat_010/tmp/transcripts.juncs /dev/null /dev/null /dev/null tophat_010/tmp/left_kept_reads.m2g_um.candidates.bam tophat_010/tmp/left_kept_reads.m2g_um_seg1.bam,tophat_010/tmp/left_kept_reads.m2g_um_seg2.bam,tophat_010/tmp/left_kept_reads.m2g_um_seg3.bam,tophat_010/tmp/left_kept_reads.m2g_um_seg4.bam,tophat_010/tmp/left_kept_reads.m2g_um_seg5.bam,tophat_010/tmp/left_kept_reads.m2g_um_seg6.bam,tophat_010/tmp/left_kept_reads.m2g_um_seg7.bam,tophat_010/tmp/left_kept_reads.m2g_um_seg8.bam,tophat_010/tmp/left_kept_reads.m2g_um_seg9.bam,tophat_010/tmp/left_kept_reads.m2g_um_seg10.bam,tophat_010/tmp/left_kept_reads.m2g_um_seg11.bam,tophat_010/tmp/left_kept_reads.m2g_um_seg12.bam,tophat_010/tmp/left_kept_reads.m2g_um_seg13.bam,tophat_010/tmp/left_kept_reads.m2g_um_seg14.bam tophat_010/tmp/left_kept_reads.m2g_um_seg1.to_spliced.bam,tophat_010/tmp/left_kept_reads.m2g_um_seg2.to_spliced.bam,tophat_010/tmp/left_kept_reads.m2g_um_seg3.to_spliced.bam,tophat_010/tmp/left_kept_reads.m2g_um_seg4.to_spliced.bam,tophat_010/tmp/left_kept_reads.m2g_um_seg5.to_spliced.bam,tophat_010/tmp/left_kept_reads.m2g_um_seg6.to_spliced.bam,tophat_010/tmp/left_kept_reads.m2g_um_seg7.to_spliced.bam,tophat_010/tmp/left_kept_reads.m2g_um_seg8.to_spliced.bam,tophat_010/tmp/left_kept_reads.m2g_um_seg9.to_spliced.bam,tophat_010/tmp/left_kept_reads.m2g_um_seg10.to_spliced.bam,tophat_010/tmp/left_kept_reads.m2g_um_seg11.to_spliced.bam,tophat_010/tmp/left_kept_reads.m2g_um_seg12.to_spliced.bam,tophat_010/tmp/left_kept_reads.m2g_um_seg13.to_spliced.bam,tophat_010/tmp/left_kept_reads.m2g_um_seg14.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 tophat_010/ --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 -p4 --gtf-annotations /data/results/reference/mmu/mm10/mRNA/transcripts.gff --gtf-juncs tophat_010/tmp/transcripts.juncs --no-closure-search --no-coverage-search --no-microexon-search --sam-header tophat_010/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/mm10/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/genome.fa tophat_010/junctions.bed tophat_010/insertions.bed tophat_010/deletions.bed tophat_010/fusions.out tophat_010/tmp/accepted_hits tophat_010/tmp/left_kept_reads.m2g.bam,tophat_010/tmp/left_kept_reads.m2g_um.mapped.bam,tophat_010/tmp/left_kept_reads.m2g_um.candidates.bam tophat_010/tmp/left_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 tophat_010/tmp/accepted_hits0.bam tophat_010/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 tophat_010/tmp/accepted_hits1.bam tophat_010/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 tophat_010/tmp/accepted_hits2.bam tophat_010/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 tophat_010/tmp/accepted_hits3.bam tophat_010/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 merge -f -h tophat_010/tmp/genome_genome.bwt.samheader.sam tophat_010/accepted_hits.bam tophat_010/tmp/accepted_hits0_sorted.bam tophat_010/tmp/accepted_hits1_sorted.bam tophat_010/tmp/accepted_hits2_sorted.bam tophat_010/tmp/accepted_hits3_sorted.bam
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-2.1.1.Linux_x86_64/bam_merge -Q --sam-header tophat_010/tmp/genome_genome.bwt.samheader.sam tophat_010/unmapped.bam tophat_010/tmp/unmapped_left_0.bam tophat_010/tmp/unmapped_left_1.bam tophat_010/tmp/unmapped_left_2.bam tophat_010/tmp/unmapped_left_3.bam
#>alldone: