/home/xianggan/bin/exoner/tophat --num-threads 4 --max-multihits 10 --coverage-search --microexon-search -o mergeall90/ small.90 mergeall90//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 mergeall90/// --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 mergeall90///tmp/stub_header.sam --fastq mergeall90//novel.all.flt_1.fq
bowtie -q --un mergeall90///tmp/left_kept_reads_missing.fq --max /dev/null -n 2 -p 4 -k 40 -m 40 small.90 mergeall90///tmp/left_kept_reads.fq | /Net/fs1/home/xianggan/bin/exoner/fix_map_ordering --fastq mergeall90///tmp/left_kept_reads.fq - > mergeall90///tmp/file2C0TeJ
/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 mergeall90/// --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 mergeall90///tmp/stub_header.sam mergeall90///tmp/small.90.fa mergeall90///tmp/left_kept_reads.fq /dev/null mergeall90///tmp/left_kept_reads.bwtout  > mergeall90///tmp/file4IatGU
bowtie -q --un mergeall90///tmp/left_kept_reads_seg1_missing.fq --max /dev/null -n 2 -p 4 -k 40 -m 40 small.90 mergeall90///tmp/left_kept_reads_seg1.fq | /Net/fs1/home/xianggan/bin/exoner/fix_map_ordering --fastq mergeall90///tmp/left_kept_reads_seg1.fq - > mergeall90///tmp/filelmNo4y
bowtie -q --un mergeall90///tmp/left_kept_reads_seg2_missing.fq --max /dev/null -n 2 -p 4 -k 40 -m 40 small.90 mergeall90///tmp/left_kept_reads_seg2.fq | /Net/fs1/home/xianggan/bin/exoner/fix_map_ordering --fastq mergeall90///tmp/left_kept_reads_seg2.fq - > mergeall90///tmp/fileKj87Lq
bowtie -q --un mergeall90///tmp/left_kept_reads_seg3_missing.fq --max /dev/null -n 2 -p 4 -k 40 -m 40 small.90 mergeall90///tmp/left_kept_reads_seg3.fq | /Net/fs1/home/xianggan/bin/exoner/fix_map_ordering --fastq mergeall90///tmp/left_kept_reads_seg3.fq - > mergeall90///tmp/fileYFFisz
/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 mergeall90/// --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 mergeall90///tmp/stub_header.sam --no-closure-search --ium-reads mergeall90///tmp/left_kept_reads_seg1_missing.fq,mergeall90///tmp/left_kept_reads_seg2_missing.fq,mergeall90///tmp/left_kept_reads_seg3_missing.fq mergeall90///tmp/small.90.fa mergeall90///tmp/segment.juncs mergeall90///tmp/left_kept_reads.fq mergeall90///tmp/left_kept_reads.bwtout mergeall90///tmp/left_kept_reads_seg1.bwtout,mergeall90///tmp/left_kept_reads_seg2.bwtout,mergeall90///tmp/left_kept_reads_seg3.bwtout
/Net/fs1/home/xianggan/bin/exoner/juncs_db 3 25 mergeall90///tmp/segment.juncs mergeall90///tmp/small.90.fa
bowtie-build mergeall90///tmp/segment_juncs.fa mergeall90///tmp/segment_juncs
bowtie -q -n 2 -p 4 -k 40 -m 40 mergeall90///tmp/segment_juncs mergeall90///tmp/left_kept_reads_seg1.fq | /Net/fs1/home/xianggan/bin/exoner/fix_map_ordering --fastq mergeall90///tmp/left_kept_reads_seg1.fq - > mergeall90///tmp/fileyGsEAf
bowtie -q -n 2 -p 4 -k 40 -m 40 mergeall90///tmp/segment_juncs mergeall90///tmp/left_kept_reads_seg2.fq | /Net/fs1/home/xianggan/bin/exoner/fix_map_ordering --fastq mergeall90///tmp/left_kept_reads_seg2.fq - > mergeall90///tmp/fileJZEcBR
bowtie -q -n 2 -p 4 -k 40 -m 40 mergeall90///tmp/segment_juncs mergeall90///tmp/left_kept_reads_seg3.fq | /Net/fs1/home/xianggan/bin/exoner/fix_map_ordering --fastq mergeall90///tmp/left_kept_reads_seg3.fq - > mergeall90///tmp/fileH6Tpqu
/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 mergeall90/// --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 mergeall90///tmp/stub_header.sam --no-closure-search mergeall90///tmp/small.90.fa mergeall90///tmp/left_kept_reads.fq mergeall90///tmp/segment.juncs mergeall90///tmp/left_kept_reads_seg1.bwtout,mergeall90///tmp/left_kept_reads_seg2.bwtout,mergeall90///tmp/left_kept_reads_seg3.bwtout mergeall90///tmp/left_kept_reads_seg1_to_spliced.bwtout,mergeall90///tmp/left_kept_reads_seg2_to_spliced.bwtout,mergeall90///tmp/left_kept_reads_seg3_to_spliced.bwtout > mergeall90///tmp/left_kept_reads.fq.candidate_hits.sam
sort -k 1,1n --temporary-directory=mergeall90///tmp/ mergeall90///tmp/file4IatGU mergeall90///tmp/left_kept_reads.fq.candidate_hits.sam > mergeall90///tmp/filetcuNEm
sort -k 1,1n --temporary-directory=mergeall90///tmp/ mergeall90///tmp/file4IatGU mergeall90///tmp/left_kept_reads.fq.candidate_hits.sam
mv mergeall90///tmp/filetcuNEm mergeall90///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 mergeall90/// --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 mergeall90///tmp/stub_header.sam --no-closure-search mergeall90///junctions.bed mergeall90///tmp/accepted_hits.sam mergeall90///tmp/left_kept_reads.fq.candidate_hits.sam mergeall90///tmp/left_kept_reads.fq
samtools view -S -b mergeall90///tmp/accepted_hits.sam > mergeall90///tmp/filejM6Aaq
samtools sort mergeall90///tmp/filejM6Aaq mergeall90///accepted_hits