/home/xianggan/bin/exoner/tophat --num-threads 4 --mate-inner-dist 38 --mate-std-dev 40 --max-multihits 10 --coverage-search --microexon-search -o ./ -G ../novel221.gtf ../novel221.contig .//can_0_unmapped.flt_1.fq
/Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/gtf_juncs ../novel221.gtf
/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 .// --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 .//tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 --gtf-annotations ../novel221.gtf --fastq .//can_0_unmapped.flt_1.fq
bowtie -q --un .//tmp/left_kept_reads_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 ../novel221.contig .//tmp/left_kept_reads.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq .//tmp/left_kept_reads.fq - > .//tmp/filexqpvN0
/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 .// --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 .//tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 --gtf-annotations ../novel221.gtf ../novel221.contig.fa .//tmp/left_kept_reads.fq /dev/null /dev/null /dev/null .//tmp/left_kept_reads.bwtout  > .//tmp/fileFSjfnv
bowtie -q --un .//tmp/left_kept_reads_seg1_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 ../novel221.contig .//tmp/left_kept_reads_seg1.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq .//tmp/left_kept_reads_seg1.fq - > .//tmp/fileNvfePI
bowtie -q --un .//tmp/left_kept_reads_seg2_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 ../novel221.contig .//tmp/left_kept_reads_seg2.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq .//tmp/left_kept_reads_seg2.fq - > .//tmp/filekeSoW6
bowtie -q --un .//tmp/left_kept_reads_seg3_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 ../novel221.contig .//tmp/left_kept_reads_seg3.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq .//tmp/left_kept_reads_seg3.fq - > .//tmp/file2XuzRF
/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 .// --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 .//tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 --gtf-annotations ../novel221.gtf --no-closure-search --ium-reads .//tmp/left_kept_reads_seg1_missing.fq,.//tmp/left_kept_reads_seg2_missing.fq,.//tmp/left_kept_reads_seg3_missing.fq ../novel221.contig.fa .//tmp/segment.juncs .//tmp/segment.insertions .//tmp/segment.deletions .//tmp/left_kept_reads.fq .//tmp/left_kept_reads.bwtout .//tmp/left_kept_reads_seg1.bwtout,.//tmp/left_kept_reads_seg2.bwtout,.//tmp/left_kept_reads_seg3.bwtout
/Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/juncs_db 3 25 .//tmp/novel221.juncs,.//tmp/segment.juncs /dev/null /dev/null ../novel221.contig.fa
bowtie-build .//tmp/segment_juncs.fa .//tmp/segment_juncs
bowtie -q -v 2 -p 4 -k 10 -m 10 .//tmp/segment_juncs .//tmp/left_kept_reads_seg1.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq .//tmp/left_kept_reads_seg1.fq - > .//tmp/file684Mar
bowtie -q -v 2 -p 4 -k 10 -m 10 .//tmp/segment_juncs .//tmp/left_kept_reads_seg2.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq .//tmp/left_kept_reads_seg2.fq - > .//tmp/file4gOrIj
bowtie -q -v 2 -p 4 -k 10 -m 10 .//tmp/segment_juncs .//tmp/left_kept_reads_seg3.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq .//tmp/left_kept_reads_seg3.fq - > .//tmp/file6IBAEj
/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 .// --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 .//tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 --gtf-annotations ../novel221.gtf --no-closure-search ../novel221.contig.fa .//tmp/left_kept_reads.fq .//tmp/novel221.juncs,.//tmp/segment.juncs /dev/null /dev/null .//tmp/left_kept_reads_seg1.bwtout,.//tmp/left_kept_reads_seg2.bwtout,.//tmp/left_kept_reads_seg3.bwtout .//tmp/left_kept_reads_seg1_to_spliced.bwtout,.//tmp/left_kept_reads_seg2_to_spliced.bwtout,.//tmp/left_kept_reads_seg3_to_spliced.bwtout > .//tmp/left_kept_reads.fq.candidate_hits.sam
sort -k 1,1n --temporary-directory=.//tmp/ .//tmp/fileFSjfnv .//tmp/left_kept_reads.fq.candidate_hits.sam > .//tmp/fileoRmCCw
sort -k 1,1n --temporary-directory=.//tmp/ .//tmp/fileFSjfnv .//tmp/left_kept_reads.fq.candidate_hits.sam
mv .//tmp/fileoRmCCw .//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 .// --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 .//tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 --gtf-annotations ../novel221.gtf --no-closure-search .//junctions.bed .//insertions.bed .//deletions.bed .//tmp/accepted_hits.sam .//tmp/left_kept_reads.fq.candidate_hits.sam .//tmp/left_kept_reads.fq
samtools view -S -b .//tmp/accepted_hits.sam > .//tmp/fileGLIXpR
samtools sort .//tmp/fileGLIXpR .//accepted_hits