/home/xianggan/bin/exoner/tophat --num-threads 4 --mate-inner-dist 38 --mate-std-dev 40 --max-multihits 10 --coverage-search --microexon-search -o ./mt_0 mt_0.novel ./mt_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 ./mt_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 ./mt_0/tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 --fastq ./mt_0/acc18_unmap.flt_1.fq
bowtie -q --un ./mt_0/tmp/left_kept_reads_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 mt_0.novel ./mt_0/tmp/left_kept_reads.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./mt_0/tmp/left_kept_reads.fq - > ./mt_0/tmp/file0r8QNj
/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 ./mt_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 ./mt_0/tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 mt_0.novel.fa ./mt_0/tmp/left_kept_reads.fq /dev/null /dev/null /dev/null ./mt_0/tmp/left_kept_reads.bwtout  > ./mt_0/tmp/filegp8Cq4
bowtie -q --un ./mt_0/tmp/left_kept_reads_seg1_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 mt_0.novel ./mt_0/tmp/left_kept_reads_seg1.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./mt_0/tmp/left_kept_reads_seg1.fq - > ./mt_0/tmp/fileZ3G5uM
bowtie -q --un ./mt_0/tmp/left_kept_reads_seg2_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 mt_0.novel ./mt_0/tmp/left_kept_reads_seg2.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./mt_0/tmp/left_kept_reads_seg2.fq - > ./mt_0/tmp/fileXKQ67s
bowtie -q --un ./mt_0/tmp/left_kept_reads_seg3_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 mt_0.novel ./mt_0/tmp/left_kept_reads_seg3.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./mt_0/tmp/left_kept_reads_seg3.fq - > ./mt_0/tmp/filelifYkA
/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 ./mt_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 ./mt_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 ./mt_0/tmp/left_kept_reads_seg1_missing.fq,./mt_0/tmp/left_kept_reads_seg2_missing.fq,./mt_0/tmp/left_kept_reads_seg3_missing.fq mt_0.novel.fa ./mt_0/tmp/segment.juncs ./mt_0/tmp/segment.insertions ./mt_0/tmp/segment.deletions ./mt_0/tmp/left_kept_reads.fq ./mt_0/tmp/left_kept_reads.bwtout ./mt_0/tmp/left_kept_reads_seg1.bwtout,./mt_0/tmp/left_kept_reads_seg2.bwtout,./mt_0/tmp/left_kept_reads_seg3.bwtout
/Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/juncs_db 3 25 ./mt_0/tmp/segment.juncs /dev/null /dev/null mt_0.novel.fa
bowtie-build ./mt_0/tmp/segment_juncs.fa ./mt_0/tmp/segment_juncs
bowtie -q -v 2 -p 4 -k 10 -m 10 ./mt_0/tmp/segment_juncs ./mt_0/tmp/left_kept_reads_seg1.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./mt_0/tmp/left_kept_reads_seg1.fq - > ./mt_0/tmp/fileYhEpvG
bowtie -q -v 2 -p 4 -k 10 -m 10 ./mt_0/tmp/segment_juncs ./mt_0/tmp/left_kept_reads_seg2.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./mt_0/tmp/left_kept_reads_seg2.fq - > ./mt_0/tmp/fileL3MNJt
bowtie -q -v 2 -p 4 -k 10 -m 10 ./mt_0/tmp/segment_juncs ./mt_0/tmp/left_kept_reads_seg3.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./mt_0/tmp/left_kept_reads_seg3.fq - > ./mt_0/tmp/filec8DCUa
/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 ./mt_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 ./mt_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 mt_0.novel.fa ./mt_0/tmp/left_kept_reads.fq ./mt_0/tmp/segment.juncs /dev/null /dev/null ./mt_0/tmp/left_kept_reads_seg1.bwtout,./mt_0/tmp/left_kept_reads_seg2.bwtout,./mt_0/tmp/left_kept_reads_seg3.bwtout ./mt_0/tmp/left_kept_reads_seg1_to_spliced.bwtout,./mt_0/tmp/left_kept_reads_seg2_to_spliced.bwtout,./mt_0/tmp/left_kept_reads_seg3_to_spliced.bwtout > ./mt_0/tmp/left_kept_reads.fq.candidate_hits.sam
sort -k 1,1n --temporary-directory=./mt_0/tmp/ ./mt_0/tmp/filegp8Cq4 ./mt_0/tmp/left_kept_reads.fq.candidate_hits.sam > ./mt_0/tmp/fileuLQZa6
sort -k 1,1n --temporary-directory=./mt_0/tmp/ ./mt_0/tmp/filegp8Cq4 ./mt_0/tmp/left_kept_reads.fq.candidate_hits.sam
mv ./mt_0/tmp/fileuLQZa6 ./mt_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 ./mt_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 ./mt_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 ./mt_0/junctions.bed ./mt_0/insertions.bed ./mt_0/deletions.bed ./mt_0/tmp/accepted_hits.sam ./mt_0/tmp/left_kept_reads.fq.candidate_hits.sam ./mt_0/tmp/left_kept_reads.fq
samtools view -S -b ./mt_0/tmp/accepted_hits.sam > ./mt_0/tmp/fileen7kfN
samtools sort ./mt_0/tmp/fileen7kfN ./mt_0/accepted_hits