/home/xianggan/bin/exoner/tophat --num-threads 4 --mate-inner-dist 38 --mate-std-dev 40 --max-multihits 10 --coverage-search --microexon-search -o ./rsch_4.col rsch_4.novel ./rsch_4.col/col0Torsch_4.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 ./rsch_4.col/ --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 ./rsch_4.col/tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 --fastq ./rsch_4.col/col0Torsch_4.flt_1.fq
bowtie -q --un ./rsch_4.col/tmp/left_kept_reads_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 rsch_4.novel ./rsch_4.col/tmp/left_kept_reads.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./rsch_4.col/tmp/left_kept_reads.fq - > ./rsch_4.col/tmp/file2cgrQI
/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 ./rsch_4.col/ --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 ./rsch_4.col/tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 rsch_4.novel.fa ./rsch_4.col/tmp/left_kept_reads.fq /dev/null /dev/null /dev/null ./rsch_4.col/tmp/left_kept_reads.bwtout  > ./rsch_4.col/tmp/fileNIaJxc
bowtie -q --un ./rsch_4.col/tmp/left_kept_reads_seg1_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 rsch_4.novel ./rsch_4.col/tmp/left_kept_reads_seg1.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./rsch_4.col/tmp/left_kept_reads_seg1.fq - > ./rsch_4.col/tmp/filebW1eI8
bowtie -q --un ./rsch_4.col/tmp/left_kept_reads_seg2_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 rsch_4.novel ./rsch_4.col/tmp/left_kept_reads_seg2.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./rsch_4.col/tmp/left_kept_reads_seg2.fq - > ./rsch_4.col/tmp/fileqS1Cx2
bowtie -q --un ./rsch_4.col/tmp/left_kept_reads_seg3_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 rsch_4.novel ./rsch_4.col/tmp/left_kept_reads_seg3.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./rsch_4.col/tmp/left_kept_reads_seg3.fq - > ./rsch_4.col/tmp/filei9VWqJ
/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 ./rsch_4.col/ --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 ./rsch_4.col/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 ./rsch_4.col/tmp/left_kept_reads_seg1_missing.fq,./rsch_4.col/tmp/left_kept_reads_seg2_missing.fq,./rsch_4.col/tmp/left_kept_reads_seg3_missing.fq rsch_4.novel.fa ./rsch_4.col/tmp/segment.juncs ./rsch_4.col/tmp/segment.insertions ./rsch_4.col/tmp/segment.deletions ./rsch_4.col/tmp/left_kept_reads.fq ./rsch_4.col/tmp/left_kept_reads.bwtout ./rsch_4.col/tmp/left_kept_reads_seg1.bwtout,./rsch_4.col/tmp/left_kept_reads_seg2.bwtout,./rsch_4.col/tmp/left_kept_reads_seg3.bwtout
/Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/juncs_db 3 25 ./rsch_4.col/tmp/segment.juncs /dev/null /dev/null rsch_4.novel.fa
bowtie-build ./rsch_4.col/tmp/segment_juncs.fa ./rsch_4.col/tmp/segment_juncs
bowtie -q -v 2 -p 4 -k 10 -m 10 ./rsch_4.col/tmp/segment_juncs ./rsch_4.col/tmp/left_kept_reads_seg1.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./rsch_4.col/tmp/left_kept_reads_seg1.fq - > ./rsch_4.col/tmp/fileooSq5e
bowtie -q -v 2 -p 4 -k 10 -m 10 ./rsch_4.col/tmp/segment_juncs ./rsch_4.col/tmp/left_kept_reads_seg2.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./rsch_4.col/tmp/left_kept_reads_seg2.fq - > ./rsch_4.col/tmp/fileBiPum9
bowtie -q -v 2 -p 4 -k 10 -m 10 ./rsch_4.col/tmp/segment_juncs ./rsch_4.col/tmp/left_kept_reads_seg3.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./rsch_4.col/tmp/left_kept_reads_seg3.fq - > ./rsch_4.col/tmp/fileSEcgxj
/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 ./rsch_4.col/ --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 ./rsch_4.col/tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 --no-closure-search rsch_4.novel.fa ./rsch_4.col/tmp/left_kept_reads.fq ./rsch_4.col/tmp/segment.juncs /dev/null /dev/null ./rsch_4.col/tmp/left_kept_reads_seg1.bwtout,./rsch_4.col/tmp/left_kept_reads_seg2.bwtout,./rsch_4.col/tmp/left_kept_reads_seg3.bwtout ./rsch_4.col/tmp/left_kept_reads_seg1_to_spliced.bwtout,./rsch_4.col/tmp/left_kept_reads_seg2_to_spliced.bwtout,./rsch_4.col/tmp/left_kept_reads_seg3_to_spliced.bwtout > ./rsch_4.col/tmp/left_kept_reads.fq.candidate_hits.sam
sort -k 1,1n --temporary-directory=./rsch_4.col/tmp/ ./rsch_4.col/tmp/fileNIaJxc ./rsch_4.col/tmp/left_kept_reads.fq.candidate_hits.sam > ./rsch_4.col/tmp/filekb34f3
sort -k 1,1n --temporary-directory=./rsch_4.col/tmp/ ./rsch_4.col/tmp/fileNIaJxc ./rsch_4.col/tmp/left_kept_reads.fq.candidate_hits.sam
mv ./rsch_4.col/tmp/filekb34f3 ./rsch_4.col/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 ./rsch_4.col/ --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 ./rsch_4.col/tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 --no-closure-search ./rsch_4.col/junctions.bed ./rsch_4.col/insertions.bed ./rsch_4.col/deletions.bed ./rsch_4.col/tmp/accepted_hits.sam ./rsch_4.col/tmp/left_kept_reads.fq.candidate_hits.sam ./rsch_4.col/tmp/left_kept_reads.fq
samtools view -S -b ./rsch_4.col/tmp/accepted_hits.sam > ./rsch_4.col/tmp/fileobusG5
samtools sort ./rsch_4.col/tmp/fileobusG5 ./rsch_4.col/accepted_hits