/home/rcorbett/aligners/tophat/tophat-1.0.13/bin/tophat -r 526 -o /projects/NBL/HS1194/311L9AAXX_3/tophat_wj -G /projects/NBL/reference_files/UCSC/all.gtf.gff3 /projects/rcorbettprj/trans_abyss/bowtie_index/hg18 /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/311L9AAXX_3_1_export.txt.fastq /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/311L9AAXX_3_2_export.txt.fastq /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/gff_juncs /projects/NBL/reference_files/UCSC/all.gtf.gff3 /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/prep_reads --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/ --max-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 --inner-dist-mean 526 --inner-dist-std-dev 20 --gff-annotations /projects/NBL/reference_files/UCSC/all.gtf.gff3 --no-microexon-search --fastq /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/311L9AAXX_3_1_export.txt.fastq /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/prep_reads --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/ --max-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 --inner-dist-mean 526 --inner-dist-std-dev 20 --gff-annotations /projects/NBL/reference_files/UCSC/all.gtf.gff3 --no-microexon-search --fastq /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/311L9AAXX_3_2_export.txt.fastq bowtie -q --un /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp//left_kept_reads_missing.fq --max /dev/null -v 2 -p 1 -k 40 -m 40 /projects/rcorbettprj/trans_abyss/bowtie_index/hg18 /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/left_kept_reads.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/left_kept_reads.fq - > /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp/filexSrNQN /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/long_spanning_reads --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/ --max-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 --inner-dist-mean 526 --inner-dist-std-dev 20 --gff-annotations /projects/NBL/reference_files/UCSC/all.gtf.gff3 --no-microexon-search /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/left_kept_reads.fq /dev/null /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp//left_kept_reads.bwtout > /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp/fileDo2sbF bowtie -q --un /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp//left_kept_reads_seg1_missing.fq --max /dev/null -v 2 -p 1 -k 40 -m 40 /projects/rcorbettprj/trans_abyss/bowtie_index/hg18 /projects/NBL/HS1194/311L9AAXX_3/tophat_wj//tmp/left_kept_reads_seg1.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1194/311L9AAXX_3/tophat_wj//tmp/left_kept_reads_seg1.fq - > /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp/fileVCQfE6 bowtie -q --un /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp//left_kept_reads_seg2_missing.fq --max /dev/null -v 2 -p 1 -k 40 -m 40 /projects/rcorbettprj/trans_abyss/bowtie_index/hg18 /projects/NBL/HS1194/311L9AAXX_3/tophat_wj//tmp/left_kept_reads_seg2.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1194/311L9AAXX_3/tophat_wj//tmp/left_kept_reads_seg2.fq - > /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp/fileD8iQTT bowtie -q --un /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp//right_kept_reads_missing.fq --max /dev/null -v 2 -p 1 -k 40 -m 40 /projects/rcorbettprj/trans_abyss/bowtie_index/hg18 /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/right_kept_reads.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/right_kept_reads.fq - > /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp/fileF4jkxG /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/long_spanning_reads --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/ --max-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 --inner-dist-mean 526 --inner-dist-std-dev 20 --gff-annotations /projects/NBL/reference_files/UCSC/all.gtf.gff3 --no-closure-search --no-microexon-search /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/right_kept_reads.fq /dev/null /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp//right_kept_reads.bwtout > /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp/filepRiPRT bowtie -q --un /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp//right_kept_reads_seg1_missing.fq --max /dev/null -v 2 -p 1 -k 40 -m 40 /projects/rcorbettprj/trans_abyss/bowtie_index/hg18 /projects/NBL/HS1194/311L9AAXX_3/tophat_wj//tmp/right_kept_reads_seg1.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1194/311L9AAXX_3/tophat_wj//tmp/right_kept_reads_seg1.fq - > /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp/fileHZHcun bowtie -q --un /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp//right_kept_reads_seg2_missing.fq --max /dev/null -v 2 -p 1 -k 40 -m 40 /projects/rcorbettprj/trans_abyss/bowtie_index/hg18 /projects/NBL/HS1194/311L9AAXX_3/tophat_wj//tmp/right_kept_reads_seg2.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1194/311L9AAXX_3/tophat_wj//tmp/right_kept_reads_seg2.fq - > /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp/fileni4ZOQ /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/segment_juncs --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/ --max-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 --inner-dist-mean 526 --inner-dist-std-dev 20 --gff-annotations /projects/NBL/reference_files/UCSC/all.gtf.gff3 --no-closure-search --no-microexon-search --ium-reads /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp//left_kept_reads_seg1_missing.fq,/projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp//left_kept_reads_seg2_missing.fq,/projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp//right_kept_reads_seg1_missing.fq,/projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp//right_kept_reads_seg2_missing.fq /projects/rcorbettprj/trans_abyss/bowtie_index/hg18.fa /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp//segment.juncs /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/left_kept_reads.fq /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp//left_kept_reads_seg1.bwtout,/projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp//left_kept_reads_seg2.bwtout /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/right_kept_reads.fq /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp//right_kept_reads_seg1.bwtout,/projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp//right_kept_reads_seg2.bwtout /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/juncs_db 3 25 /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/all.juncs,/projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp//segment.juncs /projects/rcorbettprj/trans_abyss/bowtie_index/hg18.fa bowtie-build /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp/segment_juncs.fa /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp/segment_juncs bowtie -q -v 2 -p 1 -k 40 -m 40 /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp/segment_juncs /projects/NBL/HS1194/311L9AAXX_3/tophat_wj//tmp/left_kept_reads_seg1.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1194/311L9AAXX_3/tophat_wj//tmp/left_kept_reads_seg1.fq - > /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp/filexef0B1 bowtie -q -v 2 -p 1 -k 40 -m 40 /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp/segment_juncs /projects/NBL/HS1194/311L9AAXX_3/tophat_wj//tmp/left_kept_reads_seg2.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1194/311L9AAXX_3/tophat_wj//tmp/left_kept_reads_seg2.fq - > /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp/filePsl12W /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/long_spanning_reads --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/ --max-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 --inner-dist-mean 526 --inner-dist-std-dev 20 --gff-annotations /projects/NBL/reference_files/UCSC/all.gtf.gff3 --no-closure-search --no-microexon-search /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/left_kept_reads.fq /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/all.juncs,/projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp//segment.juncs /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp//left_kept_reads_seg1.bwtout,/projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp//left_kept_reads_seg2.bwtout /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp//left_kept_reads_seg1_to_spliced.bwtout,/projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp//left_kept_reads_seg2_to_spliced.bwtout > /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/left_kept_reads.fq.candidate_hits.sam sort -k 1,1n --temporary-directory=/projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp/ /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp/fileDo2sbF /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/left_kept_reads.fq.candidate_hits.sam > /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp/fileF4qL3K mv /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp/fileF4qL3K /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/left_kept_reads.fq.candidate_hits.sam bowtie -q -v 2 -p 1 -k 40 -m 40 /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp/segment_juncs /projects/NBL/HS1194/311L9AAXX_3/tophat_wj//tmp/right_kept_reads_seg1.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1194/311L9AAXX_3/tophat_wj//tmp/right_kept_reads_seg1.fq - > /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp/fileFNfkil bowtie -q -v 2 -p 1 -k 40 -m 40 /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp/segment_juncs /projects/NBL/HS1194/311L9AAXX_3/tophat_wj//tmp/right_kept_reads_seg2.fq | /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/fix_map_ordering --fastq /projects/NBL/HS1194/311L9AAXX_3/tophat_wj//tmp/right_kept_reads_seg2.fq - > /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp/filepOXik6 /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/long_spanning_reads --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/ --max-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 --inner-dist-mean 526 --inner-dist-std-dev 20 --gff-annotations /projects/NBL/reference_files/UCSC/all.gtf.gff3 --no-closure-search --no-microexon-search /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/right_kept_reads.fq /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/all.juncs,/projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp//segment.juncs /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp//right_kept_reads_seg1.bwtout,/projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp//right_kept_reads_seg2.bwtout /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp//right_kept_reads_seg1_to_spliced.bwtout,/projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp//right_kept_reads_seg2_to_spliced.bwtout > /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/right_kept_reads.fq.candidate_hits.sam sort -k 1,1n --temporary-directory=/projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp/ /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp/filepRiPRT /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/right_kept_reads.fq.candidate_hits.sam > /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp/fileDON805 mv /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp/fileDON805 /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/right_kept_reads.fq.candidate_hits.sam /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/tophat_reports --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/ --max-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 --inner-dist-mean 526 --inner-dist-std-dev 20 --gff-annotations /projects/NBL/reference_files/UCSC/all.gtf.gff3 --no-closure-search --no-microexon-search junctions.bed accepted_hits.sam /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/left_kept_reads.fq.candidate_hits.sam /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/left_kept_reads.fq /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/right_kept_reads.fq.candidate_hits.sam /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/right_kept_reads.fq sort -k 3,3 -k 4,4n --temporary-directory=/projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp/ /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/accepted_hits.sam > mv /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/accepted_hits.sam /home/rcorbett/aligners/tophat/tophat-1.0.13/bin/wiggles /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/accepted_hits.sam /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/coverage.wig