/home/xianggan/bin/exoner/tophat --num-threads 4 --max-multihits 10 --coverage-search --microexon-search -o ./rna2contig bur_novel.fa ./rna2contig/Bur_0_nss_unmapped.sanger_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 ./rna2contig// --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 ./rna2contig//tmp/stub_header.sam --fastq ./rna2contig/Bur_0_nss_unmapped.sanger_1.fq
bowtie -q --un ./rna2contig//tmp/left_kept_reads_missing.fq --max /dev/null -n 2 -p 4 -k 40 -m 40 bur_novel.fa ./rna2contig//tmp/left_kept_reads.fq | /Net/fs1/home/xianggan/bin/exoner/fix_map_ordering --fastq ./rna2contig//tmp/left_kept_reads.fq - > ./rna2contig//tmp/fileUUsQVL
/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 ./rna2contig// --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 ./rna2contig//tmp/stub_header.sam ./rna2contig//tmp/bur_novel.fa.fa ./rna2contig//tmp/left_kept_reads.fq /dev/null ./rna2contig//tmp/left_kept_reads.bwtout  > ./rna2contig//tmp/file87kO8Z
bowtie -q --un ./rna2contig//tmp/left_kept_reads_seg1_missing.fq --max /dev/null -n 2 -p 4 -k 40 -m 40 bur_novel.fa ./rna2contig//tmp/left_kept_reads_seg1.fq | /Net/fs1/home/xianggan/bin/exoner/fix_map_ordering --fastq ./rna2contig//tmp/left_kept_reads_seg1.fq - > ./rna2contig//tmp/fileh05521
bowtie -q --un ./rna2contig//tmp/left_kept_reads_seg2_missing.fq --max /dev/null -n 2 -p 4 -k 40 -m 40 bur_novel.fa ./rna2contig//tmp/left_kept_reads_seg2.fq | /Net/fs1/home/xianggan/bin/exoner/fix_map_ordering --fastq ./rna2contig//tmp/left_kept_reads_seg2.fq - > ./rna2contig//tmp/fileIRK6qK
bowtie -q --un ./rna2contig//tmp/left_kept_reads_seg3_missing.fq --max /dev/null -n 2 -p 4 -k 40 -m 40 bur_novel.fa ./rna2contig//tmp/left_kept_reads_seg3.fq | /Net/fs1/home/xianggan/bin/exoner/fix_map_ordering --fastq ./rna2contig//tmp/left_kept_reads_seg3.fq - > ./rna2contig//tmp/fileq3ieI6
/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 ./rna2contig// --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 ./rna2contig//tmp/stub_header.sam --no-closure-search --ium-reads ./rna2contig//tmp/left_kept_reads_seg1_missing.fq,./rna2contig//tmp/left_kept_reads_seg2_missing.fq,./rna2contig//tmp/left_kept_reads_seg3_missing.fq ./rna2contig//tmp/bur_novel.fa.fa ./rna2contig//tmp/segment.juncs ./rna2contig//tmp/left_kept_reads.fq ./rna2contig//tmp/left_kept_reads.bwtout ./rna2contig//tmp/left_kept_reads_seg1.bwtout,./rna2contig//tmp/left_kept_reads_seg2.bwtout,./rna2contig//tmp/left_kept_reads_seg3.bwtout
/Net/fs1/home/xianggan/bin/exoner/juncs_db 3 25 ./rna2contig//tmp/segment.juncs ./rna2contig//tmp/bur_novel.fa.fa
bowtie-build ./rna2contig//tmp/segment_juncs.fa ./rna2contig//tmp/segment_juncs
bowtie -q -n 2 -p 4 -k 40 -m 40 ./rna2contig//tmp/segment_juncs ./rna2contig//tmp/left_kept_reads_seg1.fq | /Net/fs1/home/xianggan/bin/exoner/fix_map_ordering --fastq ./rna2contig//tmp/left_kept_reads_seg1.fq - > ./rna2contig//tmp/fileEjLWDG
bowtie -q -n 2 -p 4 -k 40 -m 40 ./rna2contig//tmp/segment_juncs ./rna2contig//tmp/left_kept_reads_seg2.fq | /Net/fs1/home/xianggan/bin/exoner/fix_map_ordering --fastq ./rna2contig//tmp/left_kept_reads_seg2.fq - > ./rna2contig//tmp/fileZLAO7y
bowtie -q -n 2 -p 4 -k 40 -m 40 ./rna2contig//tmp/segment_juncs ./rna2contig//tmp/left_kept_reads_seg3.fq | /Net/fs1/home/xianggan/bin/exoner/fix_map_ordering --fastq ./rna2contig//tmp/left_kept_reads_seg3.fq - > ./rna2contig//tmp/fileHBbnWQ
/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 ./rna2contig// --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 ./rna2contig//tmp/stub_header.sam --no-closure-search ./rna2contig//tmp/bur_novel.fa.fa ./rna2contig//tmp/left_kept_reads.fq ./rna2contig//tmp/segment.juncs ./rna2contig//tmp/left_kept_reads_seg1.bwtout,./rna2contig//tmp/left_kept_reads_seg2.bwtout,./rna2contig//tmp/left_kept_reads_seg3.bwtout ./rna2contig//tmp/left_kept_reads_seg1_to_spliced.bwtout,./rna2contig//tmp/left_kept_reads_seg2_to_spliced.bwtout,./rna2contig//tmp/left_kept_reads_seg3_to_spliced.bwtout > ./rna2contig//tmp/left_kept_reads.fq.candidate_hits.sam
sort -k 1,1n --temporary-directory=./rna2contig//tmp/ ./rna2contig//tmp/file87kO8Z ./rna2contig//tmp/left_kept_reads.fq.candidate_hits.sam > ./rna2contig//tmp/filesDwWuH
sort -k 1,1n --temporary-directory=./rna2contig//tmp/ ./rna2contig//tmp/file87kO8Z ./rna2contig//tmp/left_kept_reads.fq.candidate_hits.sam
mv ./rna2contig//tmp/filesDwWuH ./rna2contig//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 ./rna2contig// --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 ./rna2contig//tmp/stub_header.sam --no-closure-search ./rna2contig//junctions.bed ./rna2contig//tmp/accepted_hits.sam ./rna2contig//tmp/left_kept_reads.fq.candidate_hits.sam ./rna2contig//tmp/left_kept_reads.fq
samtools view -S -b ./rna2contig//tmp/accepted_hits.sam > ./rna2contig//tmp/filee1lJ7P
samtools sort ./rna2contig//tmp/filee1lJ7P ./rna2contig//accepted_hits