/home/xianggan/bin/exoner/tophat --num-threads 4 --mate-inner-dist 38 --mate-std-dev 40 --max-multihits 10 --coverage-search --microexon-search -o ./small_per90 small_per90 ./small_per90/small_per90.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 ./small_per90/ --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 ./small_per90/tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 --fastq ./small_per90/small_per90.flt_1.fq
bowtie -q --un ./small_per90/tmp/left_kept_reads_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 small_per90 ./small_per90/tmp/left_kept_reads.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./small_per90/tmp/left_kept_reads.fq - > ./small_per90/tmp/fileYodsUR
/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 ./small_per90/ --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 ./small_per90/tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 small_per90.fa ./small_per90/tmp/left_kept_reads.fq /dev/null /dev/null /dev/null ./small_per90/tmp/left_kept_reads.bwtout  > ./small_per90/tmp/fileRFmV4h
bowtie -q --un ./small_per90/tmp/left_kept_reads_seg1_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 small_per90 ./small_per90/tmp/left_kept_reads_seg1.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./small_per90/tmp/left_kept_reads_seg1.fq - > ./small_per90/tmp/fileZr2y3K
bowtie -q --un ./small_per90/tmp/left_kept_reads_seg2_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 small_per90 ./small_per90/tmp/left_kept_reads_seg2.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./small_per90/tmp/left_kept_reads_seg2.fq - > ./small_per90/tmp/fileq2BMj1
bowtie -q --un ./small_per90/tmp/left_kept_reads_seg3_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 small_per90 ./small_per90/tmp/left_kept_reads_seg3.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./small_per90/tmp/left_kept_reads_seg3.fq - > ./small_per90/tmp/fileZCy3Wf
/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 ./small_per90/ --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 ./small_per90/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 ./small_per90/tmp/left_kept_reads_seg1_missing.fq,./small_per90/tmp/left_kept_reads_seg2_missing.fq,./small_per90/tmp/left_kept_reads_seg3_missing.fq small_per90.fa ./small_per90/tmp/segment.juncs ./small_per90/tmp/segment.insertions ./small_per90/tmp/segment.deletions ./small_per90/tmp/left_kept_reads.fq ./small_per90/tmp/left_kept_reads.bwtout ./small_per90/tmp/left_kept_reads_seg1.bwtout,./small_per90/tmp/left_kept_reads_seg2.bwtout,./small_per90/tmp/left_kept_reads_seg3.bwtout
/Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/juncs_db 3 25 ./small_per90/tmp/segment.juncs /dev/null /dev/null small_per90.fa
bowtie-build ./small_per90/tmp/segment_juncs.fa ./small_per90/tmp/segment_juncs
bowtie -q -v 2 -p 4 -k 10 -m 10 ./small_per90/tmp/segment_juncs ./small_per90/tmp/left_kept_reads_seg1.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./small_per90/tmp/left_kept_reads_seg1.fq - > ./small_per90/tmp/fileUkTEVv
bowtie -q -v 2 -p 4 -k 10 -m 10 ./small_per90/tmp/segment_juncs ./small_per90/tmp/left_kept_reads_seg2.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./small_per90/tmp/left_kept_reads_seg2.fq - > ./small_per90/tmp/filevlfiy8
bowtie -q -v 2 -p 4 -k 10 -m 10 ./small_per90/tmp/segment_juncs ./small_per90/tmp/left_kept_reads_seg3.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./small_per90/tmp/left_kept_reads_seg3.fq - > ./small_per90/tmp/fileItkPNZ
/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 ./small_per90/ --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 ./small_per90/tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 --no-closure-search small_per90.fa ./small_per90/tmp/left_kept_reads.fq ./small_per90/tmp/segment.juncs /dev/null /dev/null ./small_per90/tmp/left_kept_reads_seg1.bwtout,./small_per90/tmp/left_kept_reads_seg2.bwtout,./small_per90/tmp/left_kept_reads_seg3.bwtout ./small_per90/tmp/left_kept_reads_seg1_to_spliced.bwtout,./small_per90/tmp/left_kept_reads_seg2_to_spliced.bwtout,./small_per90/tmp/left_kept_reads_seg3_to_spliced.bwtout > ./small_per90/tmp/left_kept_reads.fq.candidate_hits.sam
sort -k 1,1n --temporary-directory=./small_per90/tmp/ ./small_per90/tmp/fileRFmV4h ./small_per90/tmp/left_kept_reads.fq.candidate_hits.sam > ./small_per90/tmp/fileCY5bTa
sort -k 1,1n --temporary-directory=./small_per90/tmp/ ./small_per90/tmp/fileRFmV4h ./small_per90/tmp/left_kept_reads.fq.candidate_hits.sam
mv ./small_per90/tmp/fileCY5bTa ./small_per90/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 ./small_per90/ --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 ./small_per90/tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 --no-closure-search ./small_per90/junctions.bed ./small_per90/insertions.bed ./small_per90/deletions.bed ./small_per90/tmp/accepted_hits.sam ./small_per90/tmp/left_kept_reads.fq.candidate_hits.sam ./small_per90/tmp/left_kept_reads.fq
samtools view -S -b ./small_per90/tmp/accepted_hits.sam > ./small_per90/tmp/fileOtBo94
samtools sort ./small_per90/tmp/fileOtBo94 ./small_per90/accepted_hits