/opt/biosoftware/tophat/tophat/tophat -N 5 --read-edit-dist 5 -p 10 -o IR_Brain_07F1C1 /home/rneme/PopTranscriptomes/mapping/index/mm10 ../pSN7640219_15952_IRBrain07F1C1_1.fq.gz,../pSN7640219_15952_IRBrain07F1C1_2.fq.gz
#>prep_reads:
/opt/biosoftware/tophat/tophat-2.0.8b.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 IR_Brain_07F1C1/ --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 5 --read-gap-length 2 --read-edit-dist 5 --read-realign-edit-dist 6 --max-insertion-length 3 --max-deletion-length 3 -z gzip -p10 --no-closure-search --no-coverage-search --no-microexon-search --fastq --aux-outfile=IR_Brain_07F1C1/prep_reads.info --index-outfile=IR_Brain_07F1C1/tmp/left_kept_reads.bam.index --sam-header=IR_Brain_07F1C1/tmp/mm10_genome.bwt.samheader.sam --outfile=IR_Brain_07F1C1/tmp/left_kept_reads.bam ../pSN7640219_15952_IRBrain07F1C1_1.fq.gz,../pSN7640219_15952_IRBrain07F1C1_2.fq.gz
#>map_start:
/opt/biosoftware/tophat/tophat-2.0.8b.Linux_x86_64/bam2fastx --all --fastq IR_Brain_07F1C1/tmp/left_kept_reads.bam|/opt/biosoftware/bowtie/bowtie2/bowtie2-align -q -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,-32,0 -p 10 --sam-no-hd -x /home/rneme/PopTranscriptomes/mapping/index/mm10 -|/opt/biosoftware/tophat/tophat-2.0.8b.Linux_x86_64/fix_map_ordering --bowtie2-min-score 30 --read-mismatches 5 --read-gap-length 2 --read-edit-dist 5 --read-realign-edit-dist 6 --index-outfile IR_Brain_07F1C1/tmp/left_kept_reads.mapped.bam.index --sam-header IR_Brain_07F1C1/tmp/mm10_genome.bwt.samheader.sam - IR_Brain_07F1C1/tmp/left_kept_reads.mapped.bam IR_Brain_07F1C1/tmp/left_kept_reads_unmapped.bam
#>map_segments:
gzip -cd< IR_Brain_07F1C1/tmp/left_kept_reads_seg1.fq.z|/opt/biosoftware/bowtie/bowtie2/bowtie2-align -q -k 41 -N 1 -L 20 -p 10 --sam-no-hd -x /home/rneme/PopTranscriptomes/mapping/index/mm10 -|/opt/biosoftware/tophat/tophat-2.0.8b.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 5 --read-gap-length 2 --read-edit-dist 5 --read-realign-edit-dist 6 --index-outfile IR_Brain_07F1C1/tmp/left_kept_reads_seg1.bam.index --sam-header IR_Brain_07F1C1/tmp/mm10_genome.bwt.samheader.sam - IR_Brain_07F1C1/tmp/left_kept_reads_seg1.bam IR_Brain_07F1C1/tmp/left_kept_reads_seg1_unmapped.bam
gzip -cd< IR_Brain_07F1C1/tmp/left_kept_reads_seg2.fq.z|/opt/biosoftware/bowtie/bowtie2/bowtie2-align -q -k 41 -N 1 -L 20 -p 10 --sam-no-hd -x /home/rneme/PopTranscriptomes/mapping/index/mm10 -|/opt/biosoftware/tophat/tophat-2.0.8b.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 5 --read-gap-length 2 --read-edit-dist 5 --read-realign-edit-dist 6 --index-outfile IR_Brain_07F1C1/tmp/left_kept_reads_seg2.bam.index --sam-header IR_Brain_07F1C1/tmp/mm10_genome.bwt.samheader.sam - IR_Brain_07F1C1/tmp/left_kept_reads_seg2.bam IR_Brain_07F1C1/tmp/left_kept_reads_seg2_unmapped.bam
gzip -cd< IR_Brain_07F1C1/tmp/left_kept_reads_seg3.fq.z|/opt/biosoftware/bowtie/bowtie2/bowtie2-align -q -k 41 -N 1 -L 20 -p 10 --sam-no-hd -x /home/rneme/PopTranscriptomes/mapping/index/mm10 -|/opt/biosoftware/tophat/tophat-2.0.8b.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 5 --read-gap-length 2 --read-edit-dist 5 --read-realign-edit-dist 6 --index-outfile IR_Brain_07F1C1/tmp/left_kept_reads_seg3.bam.index --sam-header IR_Brain_07F1C1/tmp/mm10_genome.bwt.samheader.sam - IR_Brain_07F1C1/tmp/left_kept_reads_seg3.bam IR_Brain_07F1C1/tmp/left_kept_reads_seg3_unmapped.bam
gzip -cd< IR_Brain_07F1C1/tmp/left_kept_reads_seg4.fq.z|/opt/biosoftware/bowtie/bowtie2/bowtie2-align -q -k 41 -N 1 -L 20 -p 10 --sam-no-hd -x /home/rneme/PopTranscriptomes/mapping/index/mm10 -|/opt/biosoftware/tophat/tophat-2.0.8b.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 5 --read-gap-length 2 --read-edit-dist 5 --read-realign-edit-dist 6 --index-outfile IR_Brain_07F1C1/tmp/left_kept_reads_seg4.bam.index --sam-header IR_Brain_07F1C1/tmp/mm10_genome.bwt.samheader.sam - IR_Brain_07F1C1/tmp/left_kept_reads_seg4.bam IR_Brain_07F1C1/tmp/left_kept_reads_seg4_unmapped.bam
#>find_juncs:
/opt/biosoftware/tophat/tophat-2.0.8b.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 IR_Brain_07F1C1/ --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 5 --read-gap-length 2 --read-edit-dist 5 --read-realign-edit-dist 6 --max-insertion-length 3 --max-deletion-length 3 -z gzip -p10 --no-closure-search --no-coverage-search --no-microexon-search --sam-header IR_Brain_07F1C1/tmp/mm10_genome.bwt.samheader.sam --ium-reads IR_Brain_07F1C1/tmp/left_kept_reads_seg1_unmapped.bam,IR_Brain_07F1C1/tmp/left_kept_reads_seg2_unmapped.bam,IR_Brain_07F1C1/tmp/left_kept_reads_seg3_unmapped.bam,IR_Brain_07F1C1/tmp/left_kept_reads_seg4_unmapped.bam /home/rneme/PopTranscriptomes/mapping/index/mm10.fa IR_Brain_07F1C1/tmp/segment.juncs IR_Brain_07F1C1/tmp/segment.insertions IR_Brain_07F1C1/tmp/segment.deletions IR_Brain_07F1C1/tmp/segment.fusions IR_Brain_07F1C1/tmp/left_kept_reads.bam IR_Brain_07F1C1/tmp/left_kept_reads.mapped.bam IR_Brain_07F1C1/tmp/left_kept_reads_seg1.bam,IR_Brain_07F1C1/tmp/left_kept_reads_seg2.bam,IR_Brain_07F1C1/tmp/left_kept_reads_seg3.bam,IR_Brain_07F1C1/tmp/left_kept_reads_seg4.bam
#>juncs_db:
/opt/biosoftware/tophat/tophat-2.0.8b.Linux_x86_64/juncs_db 3 26 IR_Brain_07F1C1/tmp/segment.juncs /dev/null /dev/null /dev/null /home/rneme/PopTranscriptomes/mapping/index/mm10.fa > IR_Brain_07F1C1/tmp/segment_juncs.fa
/opt/biosoftware/bowtie/bowtie2/bowtie2-build IR_Brain_07F1C1/tmp/segment_juncs.fa IR_Brain_07F1C1/tmp/segment_juncs
#>map2juncs:
gzip -cd< IR_Brain_07F1C1/tmp/left_kept_reads_seg1.fq.z|/opt/biosoftware/bowtie/bowtie2/bowtie2-align -q -k 41 -N 1 -L 20 -p 10 --sam-no-hd -x IR_Brain_07F1C1/tmp/segment_juncs -|/opt/biosoftware/tophat/tophat-2.0.8b.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 5 --read-gap-length 2 --read-edit-dist 5 --read-realign-edit-dist 6 --index-outfile IR_Brain_07F1C1/tmp/left_kept_reads_seg1.to_spliced.bam.index --sam-header IR_Brain_07F1C1/tmp/segment_juncs.bwt.samheader.sam - IR_Brain_07F1C1/tmp/left_kept_reads_seg1.to_spliced.bam
gzip -cd< IR_Brain_07F1C1/tmp/left_kept_reads_seg2.fq.z|/opt/biosoftware/bowtie/bowtie2/bowtie2-align -q -k 41 -N 1 -L 20 -p 10 --sam-no-hd -x IR_Brain_07F1C1/tmp/segment_juncs -|/opt/biosoftware/tophat/tophat-2.0.8b.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 5 --read-gap-length 2 --read-edit-dist 5 --read-realign-edit-dist 6 --index-outfile IR_Brain_07F1C1/tmp/left_kept_reads_seg2.to_spliced.bam.index --sam-header IR_Brain_07F1C1/tmp/segment_juncs.bwt.samheader.sam - IR_Brain_07F1C1/tmp/left_kept_reads_seg2.to_spliced.bam
gzip -cd< IR_Brain_07F1C1/tmp/left_kept_reads_seg3.fq.z|/opt/biosoftware/bowtie/bowtie2/bowtie2-align -q -k 41 -N 1 -L 20 -p 10 --sam-no-hd -x IR_Brain_07F1C1/tmp/segment_juncs -|/opt/biosoftware/tophat/tophat-2.0.8b.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 5 --read-gap-length 2 --read-edit-dist 5 --read-realign-edit-dist 6 --index-outfile IR_Brain_07F1C1/tmp/left_kept_reads_seg3.to_spliced.bam.index --sam-header IR_Brain_07F1C1/tmp/segment_juncs.bwt.samheader.sam - IR_Brain_07F1C1/tmp/left_kept_reads_seg3.to_spliced.bam
gzip -cd< IR_Brain_07F1C1/tmp/left_kept_reads_seg4.fq.z|/opt/biosoftware/bowtie/bowtie2/bowtie2-align -q -k 41 -N 1 -L 20 -p 10 --sam-no-hd -x IR_Brain_07F1C1/tmp/segment_juncs -|/opt/biosoftware/tophat/tophat-2.0.8b.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 5 --read-gap-length 2 --read-edit-dist 5 --read-realign-edit-dist 6 --index-outfile IR_Brain_07F1C1/tmp/left_kept_reads_seg4.to_spliced.bam.index --sam-header IR_Brain_07F1C1/tmp/segment_juncs.bwt.samheader.sam - IR_Brain_07F1C1/tmp/left_kept_reads_seg4.to_spliced.bam
/opt/biosoftware/tophat/tophat-2.0.8b.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 IR_Brain_07F1C1/ --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 5 --read-gap-length 2 --read-edit-dist 5 --read-realign-edit-dist 6 --max-insertion-length 3 --max-deletion-length 3 -z gzip -p10 --no-closure-search --no-coverage-search --no-microexon-search --sam-header IR_Brain_07F1C1/tmp/mm10_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 /home/rneme/PopTranscriptomes/mapping/index/mm10.fa IR_Brain_07F1C1/tmp/left_kept_reads.bam IR_Brain_07F1C1/tmp/segment.juncs IR_Brain_07F1C1/tmp/segment.insertions IR_Brain_07F1C1/tmp/segment.deletions /dev/null IR_Brain_07F1C1/tmp/left_kept_reads.candidates.bam IR_Brain_07F1C1/tmp/left_kept_reads_seg1.bam,IR_Brain_07F1C1/tmp/left_kept_reads_seg2.bam,IR_Brain_07F1C1/tmp/left_kept_reads_seg3.bam,IR_Brain_07F1C1/tmp/left_kept_reads_seg4.bam IR_Brain_07F1C1/tmp/left_kept_reads_seg1.to_spliced.bam,IR_Brain_07F1C1/tmp/left_kept_reads_seg2.to_spliced.bam,IR_Brain_07F1C1/tmp/left_kept_reads_seg3.to_spliced.bam,IR_Brain_07F1C1/tmp/left_kept_reads_seg4.to_spliced.bam
#>tophat_reports:
/opt/biosoftware/tophat/tophat-2.0.8b.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 IR_Brain_07F1C1/ --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 5 --read-gap-length 2 --read-edit-dist 5 --read-realign-edit-dist 6 --max-insertion-length 3 --max-deletion-length 3 -z gzip -p10 --no-closure-search --no-coverage-search --no-microexon-search --sam-header IR_Brain_07F1C1/tmp/mm10_genome.bwt.samheader.sam --report-discordant-pair-alignments --report-mixed-alignments --samtools=/usr/local/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 /home/rneme/PopTranscriptomes/mapping/index/mm10.fa IR_Brain_07F1C1/junctions.bed IR_Brain_07F1C1/insertions.bed IR_Brain_07F1C1/deletions.bed IR_Brain_07F1C1/fusions.out IR_Brain_07F1C1/tmp/accepted_hits IR_Brain_07F1C1/tmp/left_kept_reads.mapped.bam,IR_Brain_07F1C1/tmp/left_kept_reads.candidates IR_Brain_07F1C1/tmp/left_kept_reads.bam
/usr/local/bin/samtools sort IR_Brain_07F1C1/tmp/accepted_hits0.bam IR_Brain_07F1C1/tmp/accepted_hits0_sorted
/usr/local/bin/samtools sort IR_Brain_07F1C1/tmp/accepted_hits1.bam IR_Brain_07F1C1/tmp/accepted_hits1_sorted
/usr/local/bin/samtools sort IR_Brain_07F1C1/tmp/accepted_hits2.bam IR_Brain_07F1C1/tmp/accepted_hits2_sorted
/usr/local/bin/samtools sort IR_Brain_07F1C1/tmp/accepted_hits3.bam IR_Brain_07F1C1/tmp/accepted_hits3_sorted
/usr/local/bin/samtools sort IR_Brain_07F1C1/tmp/accepted_hits4.bam IR_Brain_07F1C1/tmp/accepted_hits4_sorted
/usr/local/bin/samtools sort IR_Brain_07F1C1/tmp/accepted_hits5.bam IR_Brain_07F1C1/tmp/accepted_hits5_sorted
/usr/local/bin/samtools sort IR_Brain_07F1C1/tmp/accepted_hits6.bam IR_Brain_07F1C1/tmp/accepted_hits6_sorted
/usr/local/bin/samtools sort IR_Brain_07F1C1/tmp/accepted_hits7.bam IR_Brain_07F1C1/tmp/accepted_hits7_sorted
/usr/local/bin/samtools sort IR_Brain_07F1C1/tmp/accepted_hits8.bam IR_Brain_07F1C1/tmp/accepted_hits8_sorted
/usr/local/bin/samtools sort IR_Brain_07F1C1/tmp/accepted_hits9.bam IR_Brain_07F1C1/tmp/accepted_hits9_sorted
/usr/local/bin/samtools merge -f -h IR_Brain_07F1C1/tmp/mm10_genome.bwt.samheader.sam IR_Brain_07F1C1/accepted_hits.bam IR_Brain_07F1C1/tmp/accepted_hits0_sorted.bam IR_Brain_07F1C1/tmp/accepted_hits1_sorted.bam IR_Brain_07F1C1/tmp/accepted_hits2_sorted.bam IR_Brain_07F1C1/tmp/accepted_hits3_sorted.bam IR_Brain_07F1C1/tmp/accepted_hits4_sorted.bam IR_Brain_07F1C1/tmp/accepted_hits5_sorted.bam IR_Brain_07F1C1/tmp/accepted_hits6_sorted.bam IR_Brain_07F1C1/tmp/accepted_hits7_sorted.bam IR_Brain_07F1C1/tmp/accepted_hits8_sorted.bam IR_Brain_07F1C1/tmp/accepted_hits9_sorted.bam
/opt/biosoftware/tophat/tophat-2.0.8b.Linux_x86_64/bam_merge -Q --sam-header IR_Brain_07F1C1/tmp/mm10_genome.bwt.samheader.sam IR_Brain_07F1C1/unmapped.bam IR_Brain_07F1C1/tmp/unmapped_left_0.bam IR_Brain_07F1C1/tmp/unmapped_left_1.bam IR_Brain_07F1C1/tmp/unmapped_left_2.bam IR_Brain_07F1C1/tmp/unmapped_left_3.bam IR_Brain_07F1C1/tmp/unmapped_left_4.bam IR_Brain_07F1C1/tmp/unmapped_left_5.bam IR_Brain_07F1C1/tmp/unmapped_left_6.bam IR_Brain_07F1C1/tmp/unmapped_left_7.bam IR_Brain_07F1C1/tmp/unmapped_left_8.bam IR_Brain_07F1C1/tmp/unmapped_left_9.bam
#>alldone: