/home/xianggan/bin/exoner/tophat --num-threads 4 --max-multihits 10 --coverage-search --microexon-search -o Bur_0_R1/ bur_novel.fa Bur_0_R1//R38_L1_Bur_0_sdlg_R1_nss_barcode_ACG.unmap_1.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 Bur_0_R1/// --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 Bur_0_R1///tmp/stub_header.sam --fastq Bur_0_R1//R38_L1_Bur_0_sdlg_R1_nss_barcode_ACG.unmap_1.flt_1.fq
bowtie -q --un Bur_0_R1///tmp/left_kept_reads_missing.fq --max /dev/null -n 2 -p 4 -k 40 -m 40 bur_novel.fa Bur_0_R1///tmp/left_kept_reads.fq | /Net/fs1/home/xianggan/bin/exoner/fix_map_ordering --fastq Bur_0_R1///tmp/left_kept_reads.fq - > Bur_0_R1///tmp/filedlMVyS
/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 Bur_0_R1/// --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 Bur_0_R1///tmp/stub_header.sam Bur_0_R1///tmp/bur_novel.fa.fa Bur_0_R1///tmp/left_kept_reads.fq /dev/null Bur_0_R1///tmp/left_kept_reads.bwtout  > Bur_0_R1///tmp/file8b6KCY
bowtie -q --un Bur_0_R1///tmp/left_kept_reads_seg1_missing.fq --max /dev/null -n 2 -p 4 -k 40 -m 40 bur_novel.fa Bur_0_R1///tmp/left_kept_reads_seg1.fq | /Net/fs1/home/xianggan/bin/exoner/fix_map_ordering --fastq Bur_0_R1///tmp/left_kept_reads_seg1.fq - > Bur_0_R1///tmp/filelR4npp
bowtie -q --un Bur_0_R1///tmp/left_kept_reads_seg2_missing.fq --max /dev/null -n 2 -p 4 -k 40 -m 40 bur_novel.fa Bur_0_R1///tmp/left_kept_reads_seg2.fq | /Net/fs1/home/xianggan/bin/exoner/fix_map_ordering --fastq Bur_0_R1///tmp/left_kept_reads_seg2.fq - > Bur_0_R1///tmp/filekG2ii4
bowtie -q --un Bur_0_R1///tmp/left_kept_reads_seg3_missing.fq --max /dev/null -n 2 -p 4 -k 40 -m 40 bur_novel.fa Bur_0_R1///tmp/left_kept_reads_seg3.fq | /Net/fs1/home/xianggan/bin/exoner/fix_map_ordering --fastq Bur_0_R1///tmp/left_kept_reads_seg3.fq - > Bur_0_R1///tmp/filebwDnoX
/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 Bur_0_R1/// --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 Bur_0_R1///tmp/stub_header.sam --no-closure-search --ium-reads Bur_0_R1///tmp/left_kept_reads_seg1_missing.fq,Bur_0_R1///tmp/left_kept_reads_seg2_missing.fq,Bur_0_R1///tmp/left_kept_reads_seg3_missing.fq Bur_0_R1///tmp/bur_novel.fa.fa Bur_0_R1///tmp/segment.juncs Bur_0_R1///tmp/left_kept_reads.fq Bur_0_R1///tmp/left_kept_reads.bwtout Bur_0_R1///tmp/left_kept_reads_seg1.bwtout,Bur_0_R1///tmp/left_kept_reads_seg2.bwtout,Bur_0_R1///tmp/left_kept_reads_seg3.bwtout
/Net/fs1/home/xianggan/bin/exoner/juncs_db 3 25 Bur_0_R1///tmp/segment.juncs Bur_0_R1///tmp/bur_novel.fa.fa
bowtie-build Bur_0_R1///tmp/segment_juncs.fa Bur_0_R1///tmp/segment_juncs
bowtie -q -n 2 -p 4 -k 40 -m 40 Bur_0_R1///tmp/segment_juncs Bur_0_R1///tmp/left_kept_reads_seg1.fq | /Net/fs1/home/xianggan/bin/exoner/fix_map_ordering --fastq Bur_0_R1///tmp/left_kept_reads_seg1.fq - > Bur_0_R1///tmp/fileF6B35E
bowtie -q -n 2 -p 4 -k 40 -m 40 Bur_0_R1///tmp/segment_juncs Bur_0_R1///tmp/left_kept_reads_seg2.fq | /Net/fs1/home/xianggan/bin/exoner/fix_map_ordering --fastq Bur_0_R1///tmp/left_kept_reads_seg2.fq - > Bur_0_R1///tmp/filesHF7bs
bowtie -q -n 2 -p 4 -k 40 -m 40 Bur_0_R1///tmp/segment_juncs Bur_0_R1///tmp/left_kept_reads_seg3.fq | /Net/fs1/home/xianggan/bin/exoner/fix_map_ordering --fastq Bur_0_R1///tmp/left_kept_reads_seg3.fq - > Bur_0_R1///tmp/file57a5xj
/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 Bur_0_R1/// --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 Bur_0_R1///tmp/stub_header.sam --no-closure-search Bur_0_R1///tmp/bur_novel.fa.fa Bur_0_R1///tmp/left_kept_reads.fq Bur_0_R1///tmp/segment.juncs Bur_0_R1///tmp/left_kept_reads_seg1.bwtout,Bur_0_R1///tmp/left_kept_reads_seg2.bwtout,Bur_0_R1///tmp/left_kept_reads_seg3.bwtout Bur_0_R1///tmp/left_kept_reads_seg1_to_spliced.bwtout,Bur_0_R1///tmp/left_kept_reads_seg2_to_spliced.bwtout,Bur_0_R1///tmp/left_kept_reads_seg3_to_spliced.bwtout > Bur_0_R1///tmp/left_kept_reads.fq.candidate_hits.sam
sort -k 1,1n --temporary-directory=Bur_0_R1///tmp/ Bur_0_R1///tmp/file8b6KCY Bur_0_R1///tmp/left_kept_reads.fq.candidate_hits.sam > Bur_0_R1///tmp/file0MSJyj
sort -k 1,1n --temporary-directory=Bur_0_R1///tmp/ Bur_0_R1///tmp/file8b6KCY Bur_0_R1///tmp/left_kept_reads.fq.candidate_hits.sam
mv Bur_0_R1///tmp/file0MSJyj Bur_0_R1///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 Bur_0_R1/// --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 Bur_0_R1///tmp/stub_header.sam --no-closure-search Bur_0_R1///junctions.bed Bur_0_R1///tmp/accepted_hits.sam Bur_0_R1///tmp/left_kept_reads.fq.candidate_hits.sam Bur_0_R1///tmp/left_kept_reads.fq
samtools view -S -b Bur_0_R1///tmp/accepted_hits.sam > Bur_0_R1///tmp/fileZhPK7p
samtools sort Bur_0_R1///tmp/fileZhPK7p Bur_0_R1///accepted_hits