/data/results/tools/align/tophat-1.4.0.Linux_x86_64/tophat -p 10 -o wt0hrep1b -C /data/results/reference/mmu/mm9/bowtie1/mm9c ../fastq/0hrep1b.fastq
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-1.4.0.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 wt0hrep1b/ --max-multihits 20 --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 --max-mismatches 2 --sam-header wt0hrep1b/tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 -z gzip -p10 --no-closure-search --no-microexon-search --color --fastq --aux-outfile=wt0hrep1b/left_kept_reads.info ../fastq/0hrep1b.fastq | gzip -c - >wt0hrep1b/tmp/left_kept_reads.fq.z
gzip -cd< wt0hrep1b/tmp/left_kept_reads.fq.z|/usr/bin/bowtie -q -C --col-keepends --un wt0hrep1b/tmp/left_kept_reads_unmapped.fq -v 2 -p 10 -k 20 -m 20 --max /dev/null /data/results/reference/mmu/mm9/bowtie1/mm9c -|/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-1.4.0.Linux_x86_64/fix_map_ordering -|gzip -c > wt0hrep1b/tmp/left_kept_reads.bwtout.z
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-1.4.0.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 wt0hrep1b/ --max-multihits 20 --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 --max-mismatches 2 --sam-header wt0hrep1b/tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 -z gzip -p10 --no-closure-search --no-coverage-search --no-microexon-search --color /data/results/reference/mmu/mm9/bowtie1/mm9c.fa wt0hrep1b/tmp/left_kept_reads.fq.z /dev/null /dev/null /dev/null wt0hrep1b/tmp/left_kept_reads.bwtout.z > wt0hrep1b/tmp/left_kept_reads.unspl.bam
gzip -cd< wt0hrep1b/tmp/left_kept_reads_seg1.fq.z|/usr/bin/bowtie -q -C --col-keepends --un wt0hrep1b/tmp/left_kept_reads_seg1_unmapped.fq -v 2 -p 10 -k 40 -m 40 --max /dev/null /data/results/reference/mmu/mm9/bowtie1/mm9c -|/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-1.4.0.Linux_x86_64/fix_map_ordering -|gzip -c > wt0hrep1b/tmp/left_kept_reads_seg1.bwtout.z
gzip -cd< wt0hrep1b/tmp/left_kept_reads_seg2.fq.z|/usr/bin/bowtie -q -C --col-keepends --un wt0hrep1b/tmp/left_kept_reads_seg2_unmapped.fq -v 2 -p 10 -k 40 -m 40 --max /dev/null /data/results/reference/mmu/mm9/bowtie1/mm9c -|/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-1.4.0.Linux_x86_64/fix_map_ordering -|gzip -c > wt0hrep1b/tmp/left_kept_reads_seg2.bwtout.z
gzip -cd< wt0hrep1b/tmp/left_kept_reads_seg3.fq.z|/usr/bin/bowtie -q -C --col-keepends --un wt0hrep1b/tmp/left_kept_reads_seg3_unmapped.fq -v 2 -p 10 -k 40 -m 40 --max /dev/null /data/results/reference/mmu/mm9/bowtie1/mm9c -|/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-1.4.0.Linux_x86_64/fix_map_ordering -|gzip -c > wt0hrep1b/tmp/left_kept_reads_seg3.bwtout.z
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-1.4.0.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 wt0hrep1b/ --max-multihits 20 --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 --max-mismatches 2 --sam-header wt0hrep1b/tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 -z gzip -p10 --no-closure-search --no-coverage-search --no-microexon-search --color --ium-reads wt0hrep1b/tmp/left_kept_reads_seg1_unmapped.fq,wt0hrep1b/tmp/left_kept_reads_seg2_unmapped.fq,wt0hrep1b/tmp/left_kept_reads_seg3_unmapped.fq /data/results/reference/mmu/mm9/bowtie1/mm9c.fa wt0hrep1b/tmp/segment.juncs wt0hrep1b/tmp/segment.insertions wt0hrep1b/tmp/segment.deletions wt0hrep1b/tmp/left_kept_reads.fq.z wt0hrep1b/tmp/left_kept_reads.bwtout.z wt0hrep1b/tmp/left_kept_reads_seg1.bwtout.z,wt0hrep1b/tmp/left_kept_reads_seg2.bwtout.z,wt0hrep1b/tmp/left_kept_reads_seg3.bwtout.z
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-1.4.0.Linux_x86_64/juncs_db 3 25 wt0hrep1b/tmp/segment.juncs /dev/null wt0hrep1b/tmp/segment.deletions /data/results/reference/mmu/mm9/bowtie1/mm9c.fa
/usr/bin/bowtie-build -C wt0hrep1b/tmp/segment_juncs.fa wt0hrep1b/tmp/segment_juncs
gzip -cd< wt0hrep1b/tmp/left_kept_reads_seg1.fq.z|/usr/bin/bowtie -q -C --col-keepends -v 2 -p 10 -k 40 -m 40 --max /dev/null wt0hrep1b/tmp/segment_juncs -|/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-1.4.0.Linux_x86_64/fix_map_ordering -|gzip -c > wt0hrep1b/tmp/left_kept_reads_seg1.to_spliced.bwtout.z
gzip -cd< wt0hrep1b/tmp/left_kept_reads_seg2.fq.z|/usr/bin/bowtie -q -C --col-keepends -v 2 -p 10 -k 40 -m 40 --max /dev/null wt0hrep1b/tmp/segment_juncs -|/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-1.4.0.Linux_x86_64/fix_map_ordering -|gzip -c > wt0hrep1b/tmp/left_kept_reads_seg2.to_spliced.bwtout.z
gzip -cd< wt0hrep1b/tmp/left_kept_reads_seg3.fq.z|/usr/bin/bowtie -q -C --col-keepends -v 2 -p 10 -k 40 -m 40 --max /dev/null wt0hrep1b/tmp/segment_juncs -|/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-1.4.0.Linux_x86_64/fix_map_ordering -|gzip -c > wt0hrep1b/tmp/left_kept_reads_seg3.to_spliced.bwtout.z
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-1.4.0.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 wt0hrep1b/ --max-multihits 20 --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 --max-mismatches 2 --sam-header wt0hrep1b/tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 -z gzip -p10 --no-closure-search --no-coverage-search --no-microexon-search --color /data/results/reference/mmu/mm9/bowtie1/mm9c.fa wt0hrep1b/tmp/left_kept_reads.fq.z wt0hrep1b/tmp/segment.juncs /dev/null wt0hrep1b/tmp/segment.deletions wt0hrep1b/tmp/left_kept_reads_seg1.bwtout.z,wt0hrep1b/tmp/left_kept_reads_seg2.bwtout.z,wt0hrep1b/tmp/left_kept_reads_seg3.bwtout.z wt0hrep1b/tmp/left_kept_reads_seg1.to_spliced.bwtout.z,wt0hrep1b/tmp/left_kept_reads_seg2.to_spliced.bwtout.z,wt0hrep1b/tmp/left_kept_reads_seg3.to_spliced.bwtout.z > wt0hrep1b/tmp/left_kept_reads.candidates.bam
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-1.4.0.Linux_x86_64/bam_merge wt0hrep1b/tmp/left_kept_reads.candidates_and_unspl.bam wt0hrep1b/tmp/left_kept_reads.candidates.bam wt0hrep1b/tmp/left_kept_reads.unspl.bam
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-1.4.0.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 wt0hrep1b/ --max-multihits 20 --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 --max-mismatches 2 --sam-header wt0hrep1b/tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 -z gzip -p10 --no-closure-search --no-coverage-search --no-microexon-search --color --samtools=/usr/bin/samtools wt0hrep1b/junctions.bed wt0hrep1b/insertions.bed wt0hrep1b/deletions.bed - wt0hrep1b/tmp/left_kept_reads.candidates_and_unspl.bam wt0hrep1b/tmp/left_kept_reads.fq.z | /usr/bin/samtools sort - wt0hrep1b/accepted_hits