/home/xianggan/bin/exoner/tophat --num-threads 4 --max-multihits 10 --coverage-search --microexon-search -o all18/ ngene.fa all18//novel.all.flt_1.fq
/Net/fs1/home/xianggan/bin/exoner/prep_reads --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir all18/// --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 --sam-header all18///tmp/stub_header.sam --fastq all18//novel.all.flt_1.fq
bowtie -q --un all18///tmp/left_kept_reads_missing.fq --max /dev/null -n 2 -p 4 -k 40 -m 40 ngene.fa all18///tmp/left_kept_reads.fq | /Net/fs1/home/xianggan/bin/exoner/fix_map_ordering --fastq all18///tmp/left_kept_reads.fq - > all18///tmp/fileOIb8FY
/Net/fs1/home/xianggan/bin/exoner/long_spanning_reads --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir all18/// --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 --sam-header all18///tmp/stub_header.sam all18///tmp/ngene.fa.fa all18///tmp/left_kept_reads.fq /dev/null all18///tmp/left_kept_reads.bwtout  > all18///tmp/file4VgSIh
bowtie -q --un all18///tmp/left_kept_reads_seg1_missing.fq --max /dev/null -n 2 -p 4 -k 40 -m 40 ngene.fa all18///tmp/left_kept_reads_seg1.fq | /Net/fs1/home/xianggan/bin/exoner/fix_map_ordering --fastq all18///tmp/left_kept_reads_seg1.fq - > all18///tmp/fileGFrPqq
bowtie -q --un all18///tmp/left_kept_reads_seg2_missing.fq --max /dev/null -n 2 -p 4 -k 40 -m 40 ngene.fa all18///tmp/left_kept_reads_seg2.fq | /Net/fs1/home/xianggan/bin/exoner/fix_map_ordering --fastq all18///tmp/left_kept_reads_seg2.fq - > all18///tmp/fileeMu80K
bowtie -q --un all18///tmp/left_kept_reads_seg3_missing.fq --max /dev/null -n 2 -p 4 -k 40 -m 40 ngene.fa all18///tmp/left_kept_reads_seg3.fq | /Net/fs1/home/xianggan/bin/exoner/fix_map_ordering --fastq all18///tmp/left_kept_reads_seg3.fq - > all18///tmp/fileIvM0zu
/Net/fs1/home/xianggan/bin/exoner/segment_juncs --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir all18/// --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 --sam-header all18///tmp/stub_header.sam --no-closure-search --ium-reads all18///tmp/left_kept_reads_seg1_missing.fq,all18///tmp/left_kept_reads_seg2_missing.fq,all18///tmp/left_kept_reads_seg3_missing.fq all18///tmp/ngene.fa.fa all18///tmp/segment.juncs all18///tmp/left_kept_reads.fq all18///tmp/left_kept_reads.bwtout all18///tmp/left_kept_reads_seg1.bwtout,all18///tmp/left_kept_reads_seg2.bwtout,all18///tmp/left_kept_reads_seg3.bwtout
/Net/fs1/home/xianggan/bin/exoner/juncs_db 3 25 all18///tmp/segment.juncs all18///tmp/ngene.fa.fa
bowtie-build all18///tmp/segment_juncs.fa all18///tmp/segment_juncs
bowtie -q -n 2 -p 4 -k 40 -m 40 all18///tmp/segment_juncs all18///tmp/left_kept_reads_seg1.fq | /Net/fs1/home/xianggan/bin/exoner/fix_map_ordering --fastq all18///tmp/left_kept_reads_seg1.fq - > all18///tmp/file8RP49y
bowtie -q -n 2 -p 4 -k 40 -m 40 all18///tmp/segment_juncs all18///tmp/left_kept_reads_seg2.fq | /Net/fs1/home/xianggan/bin/exoner/fix_map_ordering --fastq all18///tmp/left_kept_reads_seg2.fq - > all18///tmp/fileWZ51g0
bowtie -q -n 2 -p 4 -k 40 -m 40 all18///tmp/segment_juncs all18///tmp/left_kept_reads_seg3.fq | /Net/fs1/home/xianggan/bin/exoner/fix_map_ordering --fastq all18///tmp/left_kept_reads_seg3.fq - > all18///tmp/fileE8XWB0
/Net/fs1/home/xianggan/bin/exoner/long_spanning_reads --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir all18/// --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 --sam-header all18///tmp/stub_header.sam --no-closure-search all18///tmp/ngene.fa.fa all18///tmp/left_kept_reads.fq all18///tmp/segment.juncs all18///tmp/left_kept_reads_seg1.bwtout,all18///tmp/left_kept_reads_seg2.bwtout,all18///tmp/left_kept_reads_seg3.bwtout all18///tmp/left_kept_reads_seg1_to_spliced.bwtout,all18///tmp/left_kept_reads_seg2_to_spliced.bwtout,all18///tmp/left_kept_reads_seg3_to_spliced.bwtout > all18///tmp/left_kept_reads.fq.candidate_hits.sam
sort -k 1,1n --temporary-directory=all18///tmp/ all18///tmp/file4VgSIh all18///tmp/left_kept_reads.fq.candidate_hits.sam > all18///tmp/fileckiUay
sort -k 1,1n --temporary-directory=all18///tmp/ all18///tmp/file4VgSIh all18///tmp/left_kept_reads.fq.candidate_hits.sam
mv all18///tmp/fileckiUay all18///tmp/left_kept_reads.fq.candidate_hits.sam
/Net/fs1/home/xianggan/bin/exoner/tophat_reports --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir all18/// --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 --sam-header all18///tmp/stub_header.sam --no-closure-search all18///junctions.bed all18///tmp/accepted_hits.sam all18///tmp/left_kept_reads.fq.candidate_hits.sam all18///tmp/left_kept_reads.fq
samtools view -S -b all18///tmp/accepted_hits.sam > all18///tmp/filele8i2R
samtools sort all18///tmp/filele8i2R all18///accepted_hits