/home/xianggan/bin/exoner/tophat --num-threads 4 --mate-inner-dist 38 --mate-std-dev 40 --max-multihits 10 --coverage-search --microexon-search -o Can_0_direct2rna/ ../novelgene.v2 Can_0_direct2rna//Run33_lane1_Can_0_seedling.fastq.unmap_1.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 Can_0_direct2rna// --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 Can_0_direct2rna//tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 --fastq Can_0_direct2rna//Run33_lane1_Can_0_seedling.fastq.unmap_1.flt_1.fq
bowtie -q --un Can_0_direct2rna//tmp/left_kept_reads_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 ../novelgene.v2 Can_0_direct2rna//tmp/left_kept_reads.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Can_0_direct2rna//tmp/left_kept_reads.fq - > Can_0_direct2rna//tmp/fileJZ1dB8
/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 Can_0_direct2rna// --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 Can_0_direct2rna//tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 ../novelgene.v2.fa Can_0_direct2rna//tmp/left_kept_reads.fq /dev/null /dev/null /dev/null Can_0_direct2rna//tmp/left_kept_reads.bwtout  > Can_0_direct2rna//tmp/filecO0pNi
bowtie -q --un Can_0_direct2rna//tmp/left_kept_reads_seg1_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 ../novelgene.v2 Can_0_direct2rna//tmp/left_kept_reads_seg1.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Can_0_direct2rna//tmp/left_kept_reads_seg1.fq - > Can_0_direct2rna//tmp/fileS18Et9
bowtie -q --un Can_0_direct2rna//tmp/left_kept_reads_seg2_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 ../novelgene.v2 Can_0_direct2rna//tmp/left_kept_reads_seg2.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Can_0_direct2rna//tmp/left_kept_reads_seg2.fq - > Can_0_direct2rna//tmp/filemo1QGl
bowtie -q --un Can_0_direct2rna//tmp/left_kept_reads_seg3_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 ../novelgene.v2 Can_0_direct2rna//tmp/left_kept_reads_seg3.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Can_0_direct2rna//tmp/left_kept_reads_seg3.fq - > Can_0_direct2rna//tmp/fileNtYATO
/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 Can_0_direct2rna// --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 Can_0_direct2rna//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 Can_0_direct2rna//tmp/left_kept_reads_seg1_missing.fq,Can_0_direct2rna//tmp/left_kept_reads_seg2_missing.fq,Can_0_direct2rna//tmp/left_kept_reads_seg3_missing.fq ../novelgene.v2.fa Can_0_direct2rna//tmp/segment.juncs Can_0_direct2rna//tmp/segment.insertions Can_0_direct2rna//tmp/segment.deletions Can_0_direct2rna//tmp/left_kept_reads.fq Can_0_direct2rna//tmp/left_kept_reads.bwtout Can_0_direct2rna//tmp/left_kept_reads_seg1.bwtout,Can_0_direct2rna//tmp/left_kept_reads_seg2.bwtout,Can_0_direct2rna//tmp/left_kept_reads_seg3.bwtout
/Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/juncs_db 3 25 Can_0_direct2rna//tmp/segment.juncs /dev/null /dev/null ../novelgene.v2.fa
bowtie-build Can_0_direct2rna//tmp/segment_juncs.fa Can_0_direct2rna//tmp/segment_juncs
bowtie -q -v 2 -p 4 -k 10 -m 10 Can_0_direct2rna//tmp/segment_juncs Can_0_direct2rna//tmp/left_kept_reads_seg1.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Can_0_direct2rna//tmp/left_kept_reads_seg1.fq - > Can_0_direct2rna//tmp/fileYfiJXa
bowtie -q -v 2 -p 4 -k 10 -m 10 Can_0_direct2rna//tmp/segment_juncs Can_0_direct2rna//tmp/left_kept_reads_seg2.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Can_0_direct2rna//tmp/left_kept_reads_seg2.fq - > Can_0_direct2rna//tmp/fileTwuT4l
bowtie -q -v 2 -p 4 -k 10 -m 10 Can_0_direct2rna//tmp/segment_juncs Can_0_direct2rna//tmp/left_kept_reads_seg3.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Can_0_direct2rna//tmp/left_kept_reads_seg3.fq - > Can_0_direct2rna//tmp/filew1ub9w
/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 Can_0_direct2rna// --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 Can_0_direct2rna//tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 --no-closure-search ../novelgene.v2.fa Can_0_direct2rna//tmp/left_kept_reads.fq Can_0_direct2rna//tmp/segment.juncs /dev/null /dev/null Can_0_direct2rna//tmp/left_kept_reads_seg1.bwtout,Can_0_direct2rna//tmp/left_kept_reads_seg2.bwtout,Can_0_direct2rna//tmp/left_kept_reads_seg3.bwtout Can_0_direct2rna//tmp/left_kept_reads_seg1_to_spliced.bwtout,Can_0_direct2rna//tmp/left_kept_reads_seg2_to_spliced.bwtout,Can_0_direct2rna//tmp/left_kept_reads_seg3_to_spliced.bwtout > Can_0_direct2rna//tmp/left_kept_reads.fq.candidate_hits.sam
sort -k 1,1n --temporary-directory=Can_0_direct2rna//tmp/ Can_0_direct2rna//tmp/filecO0pNi Can_0_direct2rna//tmp/left_kept_reads.fq.candidate_hits.sam > Can_0_direct2rna//tmp/file7s0Oyd
sort -k 1,1n --temporary-directory=Can_0_direct2rna//tmp/ Can_0_direct2rna//tmp/filecO0pNi Can_0_direct2rna//tmp/left_kept_reads.fq.candidate_hits.sam
mv Can_0_direct2rna//tmp/file7s0Oyd Can_0_direct2rna//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 Can_0_direct2rna// --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 Can_0_direct2rna//tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 --no-closure-search Can_0_direct2rna//junctions.bed Can_0_direct2rna//insertions.bed Can_0_direct2rna//deletions.bed Can_0_direct2rna//tmp/accepted_hits.sam Can_0_direct2rna//tmp/left_kept_reads.fq.candidate_hits.sam Can_0_direct2rna//tmp/left_kept_reads.fq
samtools view -S -b Can_0_direct2rna//tmp/accepted_hits.sam > Can_0_direct2rna//tmp/file5tJwiy
samtools sort Can_0_direct2rna//tmp/file5tJwiy Can_0_direct2rna//accepted_hits