/home/xianggan/bin/exoner/tophat --num-threads 4 --mate-inner-dist 38 --mate-std-dev 40 --max-multihits 10 --coverage-search --microexon-search -o ./po_0 po_0.novel ./po_0/acc18_unmap.flt_1.fq
/Net/fs1/home/xianggan/bin/tophat-1.2.0.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 ./po_0/ --max-multihits 10 --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 --sam-header ./po_0/tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 --fastq ./po_0/acc18_unmap.flt_1.fq
bowtie -q --un ./po_0/tmp/left_kept_reads_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 po_0.novel ./po_0/tmp/left_kept_reads.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./po_0/tmp/left_kept_reads.fq - > ./po_0/tmp/fileXuL2bU
/Net/fs1/home/xianggan/bin/tophat-1.2.0.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 ./po_0/ --max-multihits 10 --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 --sam-header ./po_0/tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 po_0.novel.fa ./po_0/tmp/left_kept_reads.fq /dev/null /dev/null /dev/null ./po_0/tmp/left_kept_reads.bwtout  > ./po_0/tmp/filet1sZk3
bowtie -q --un ./po_0/tmp/left_kept_reads_seg1_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 po_0.novel ./po_0/tmp/left_kept_reads_seg1.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./po_0/tmp/left_kept_reads_seg1.fq - > ./po_0/tmp/fileFK9Ji8
bowtie -q --un ./po_0/tmp/left_kept_reads_seg2_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 po_0.novel ./po_0/tmp/left_kept_reads_seg2.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./po_0/tmp/left_kept_reads_seg2.fq - > ./po_0/tmp/fileFT8LV3
bowtie -q --un ./po_0/tmp/left_kept_reads_seg3_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 po_0.novel ./po_0/tmp/left_kept_reads_seg3.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./po_0/tmp/left_kept_reads_seg3.fq - > ./po_0/tmp/filequAFaB
/Net/fs1/home/xianggan/bin/tophat-1.2.0.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 ./po_0/ --max-multihits 10 --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 --sam-header ./po_0/tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 --no-closure-search --ium-reads ./po_0/tmp/left_kept_reads_seg1_missing.fq,./po_0/tmp/left_kept_reads_seg2_missing.fq,./po_0/tmp/left_kept_reads_seg3_missing.fq po_0.novel.fa ./po_0/tmp/segment.juncs ./po_0/tmp/segment.insertions ./po_0/tmp/segment.deletions ./po_0/tmp/left_kept_reads.fq ./po_0/tmp/left_kept_reads.bwtout ./po_0/tmp/left_kept_reads_seg1.bwtout,./po_0/tmp/left_kept_reads_seg2.bwtout,./po_0/tmp/left_kept_reads_seg3.bwtout
/Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/juncs_db 3 25 ./po_0/tmp/segment.juncs /dev/null /dev/null po_0.novel.fa
bowtie-build ./po_0/tmp/segment_juncs.fa ./po_0/tmp/segment_juncs
bowtie -q -v 2 -p 4 -k 10 -m 10 ./po_0/tmp/segment_juncs ./po_0/tmp/left_kept_reads_seg1.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./po_0/tmp/left_kept_reads_seg1.fq - > ./po_0/tmp/filew8v0yy
bowtie -q -v 2 -p 4 -k 10 -m 10 ./po_0/tmp/segment_juncs ./po_0/tmp/left_kept_reads_seg2.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./po_0/tmp/left_kept_reads_seg2.fq - > ./po_0/tmp/file3yjEgT
bowtie -q -v 2 -p 4 -k 10 -m 10 ./po_0/tmp/segment_juncs ./po_0/tmp/left_kept_reads_seg3.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./po_0/tmp/left_kept_reads_seg3.fq - > ./po_0/tmp/filesOCu8Q
/Net/fs1/home/xianggan/bin/tophat-1.2.0.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 ./po_0/ --max-multihits 10 --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 --sam-header ./po_0/tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 --no-closure-search po_0.novel.fa ./po_0/tmp/left_kept_reads.fq ./po_0/tmp/segment.juncs /dev/null /dev/null ./po_0/tmp/left_kept_reads_seg1.bwtout,./po_0/tmp/left_kept_reads_seg2.bwtout,./po_0/tmp/left_kept_reads_seg3.bwtout ./po_0/tmp/left_kept_reads_seg1_to_spliced.bwtout,./po_0/tmp/left_kept_reads_seg2_to_spliced.bwtout,./po_0/tmp/left_kept_reads_seg3_to_spliced.bwtout > ./po_0/tmp/left_kept_reads.fq.candidate_hits.sam
sort -k 1,1n --temporary-directory=./po_0/tmp/ ./po_0/tmp/filet1sZk3 ./po_0/tmp/left_kept_reads.fq.candidate_hits.sam > ./po_0/tmp/fileCQGqKY
sort -k 1,1n --temporary-directory=./po_0/tmp/ ./po_0/tmp/filet1sZk3 ./po_0/tmp/left_kept_reads.fq.candidate_hits.sam
mv ./po_0/tmp/fileCQGqKY ./po_0/tmp/left_kept_reads.fq.candidate_hits.sam
/Net/fs1/home/xianggan/bin/tophat-1.2.0.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 ./po_0/ --max-multihits 10 --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 --sam-header ./po_0/tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 --no-closure-search ./po_0/junctions.bed ./po_0/insertions.bed ./po_0/deletions.bed ./po_0/tmp/accepted_hits.sam ./po_0/tmp/left_kept_reads.fq.candidate_hits.sam ./po_0/tmp/left_kept_reads.fq
samtools view -S -b ./po_0/tmp/accepted_hits.sam > ./po_0/tmp/fileIoTBRQ
samtools sort ./po_0/tmp/fileIoTBRQ ./po_0/accepted_hits