/home/xianggan/bin/exoner/tophat --num-threads 4 --mate-inner-dist 38 --mate-std-dev 40 --max-multihits 10 --coverage-search --microexon-search -o ./Hi_0_R2.TOnovel ../novelgene.v2 ./Hi_0_R2.TOnovel/R38_L4_Hi_0_sdlg_R2_nss_barcode_CAT.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 ./Hi_0_R2.TOnovel/ --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 ./Hi_0_R2.TOnovel/tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 --fastq ./Hi_0_R2.TOnovel/R38_L4_Hi_0_sdlg_R2_nss_barcode_CAT.unmap_1.flt_1.fq
bowtie -q --un ./Hi_0_R2.TOnovel/tmp/left_kept_reads_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 ../novelgene.v2 ./Hi_0_R2.TOnovel/tmp/left_kept_reads.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./Hi_0_R2.TOnovel/tmp/left_kept_reads.fq - > ./Hi_0_R2.TOnovel/tmp/fileGTSbTt
/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 ./Hi_0_R2.TOnovel/ --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 ./Hi_0_R2.TOnovel/tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 ../novelgene.v2.fa ./Hi_0_R2.TOnovel/tmp/left_kept_reads.fq /dev/null /dev/null /dev/null ./Hi_0_R2.TOnovel/tmp/left_kept_reads.bwtout  > ./Hi_0_R2.TOnovel/tmp/filewxwG5T
bowtie -q --un ./Hi_0_R2.TOnovel/tmp/left_kept_reads_seg1_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 ../novelgene.v2 ./Hi_0_R2.TOnovel/tmp/left_kept_reads_seg1.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./Hi_0_R2.TOnovel/tmp/left_kept_reads_seg1.fq - > ./Hi_0_R2.TOnovel/tmp/fileoKidGE
bowtie -q --un ./Hi_0_R2.TOnovel/tmp/left_kept_reads_seg2_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 ../novelgene.v2 ./Hi_0_R2.TOnovel/tmp/left_kept_reads_seg2.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./Hi_0_R2.TOnovel/tmp/left_kept_reads_seg2.fq - > ./Hi_0_R2.TOnovel/tmp/fileJ1jW6t
bowtie -q --un ./Hi_0_R2.TOnovel/tmp/left_kept_reads_seg3_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 ../novelgene.v2 ./Hi_0_R2.TOnovel/tmp/left_kept_reads_seg3.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./Hi_0_R2.TOnovel/tmp/left_kept_reads_seg3.fq - > ./Hi_0_R2.TOnovel/tmp/fileRilEno
/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 ./Hi_0_R2.TOnovel/ --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 ./Hi_0_R2.TOnovel/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 ./Hi_0_R2.TOnovel/tmp/left_kept_reads_seg1_missing.fq,./Hi_0_R2.TOnovel/tmp/left_kept_reads_seg2_missing.fq,./Hi_0_R2.TOnovel/tmp/left_kept_reads_seg3_missing.fq ../novelgene.v2.fa ./Hi_0_R2.TOnovel/tmp/segment.juncs ./Hi_0_R2.TOnovel/tmp/segment.insertions ./Hi_0_R2.TOnovel/tmp/segment.deletions ./Hi_0_R2.TOnovel/tmp/left_kept_reads.fq ./Hi_0_R2.TOnovel/tmp/left_kept_reads.bwtout ./Hi_0_R2.TOnovel/tmp/left_kept_reads_seg1.bwtout,./Hi_0_R2.TOnovel/tmp/left_kept_reads_seg2.bwtout,./Hi_0_R2.TOnovel/tmp/left_kept_reads_seg3.bwtout
/Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/juncs_db 3 25 ./Hi_0_R2.TOnovel/tmp/segment.juncs /dev/null /dev/null ../novelgene.v2.fa
bowtie-build ./Hi_0_R2.TOnovel/tmp/segment_juncs.fa ./Hi_0_R2.TOnovel/tmp/segment_juncs
bowtie -q -v 2 -p 4 -k 10 -m 10 ./Hi_0_R2.TOnovel/tmp/segment_juncs ./Hi_0_R2.TOnovel/tmp/left_kept_reads_seg1.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./Hi_0_R2.TOnovel/tmp/left_kept_reads_seg1.fq - > ./Hi_0_R2.TOnovel/tmp/fileLQGXdR
bowtie -q -v 2 -p 4 -k 10 -m 10 ./Hi_0_R2.TOnovel/tmp/segment_juncs ./Hi_0_R2.TOnovel/tmp/left_kept_reads_seg2.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./Hi_0_R2.TOnovel/tmp/left_kept_reads_seg2.fq - > ./Hi_0_R2.TOnovel/tmp/fileAed0qm
bowtie -q -v 2 -p 4 -k 10 -m 10 ./Hi_0_R2.TOnovel/tmp/segment_juncs ./Hi_0_R2.TOnovel/tmp/left_kept_reads_seg3.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./Hi_0_R2.TOnovel/tmp/left_kept_reads_seg3.fq - > ./Hi_0_R2.TOnovel/tmp/fileR36w4T
/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 ./Hi_0_R2.TOnovel/ --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 ./Hi_0_R2.TOnovel/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 ./Hi_0_R2.TOnovel/tmp/left_kept_reads.fq ./Hi_0_R2.TOnovel/tmp/segment.juncs /dev/null /dev/null ./Hi_0_R2.TOnovel/tmp/left_kept_reads_seg1.bwtout,./Hi_0_R2.TOnovel/tmp/left_kept_reads_seg2.bwtout,./Hi_0_R2.TOnovel/tmp/left_kept_reads_seg3.bwtout ./Hi_0_R2.TOnovel/tmp/left_kept_reads_seg1_to_spliced.bwtout,./Hi_0_R2.TOnovel/tmp/left_kept_reads_seg2_to_spliced.bwtout,./Hi_0_R2.TOnovel/tmp/left_kept_reads_seg3_to_spliced.bwtout > ./Hi_0_R2.TOnovel/tmp/left_kept_reads.fq.candidate_hits.sam
sort -k 1,1n --temporary-directory=./Hi_0_R2.TOnovel/tmp/ ./Hi_0_R2.TOnovel/tmp/filewxwG5T ./Hi_0_R2.TOnovel/tmp/left_kept_reads.fq.candidate_hits.sam > ./Hi_0_R2.TOnovel/tmp/fileDuSpQw
sort -k 1,1n --temporary-directory=./Hi_0_R2.TOnovel/tmp/ ./Hi_0_R2.TOnovel/tmp/filewxwG5T ./Hi_0_R2.TOnovel/tmp/left_kept_reads.fq.candidate_hits.sam
mv ./Hi_0_R2.TOnovel/tmp/fileDuSpQw ./Hi_0_R2.TOnovel/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 ./Hi_0_R2.TOnovel/ --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 ./Hi_0_R2.TOnovel/tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 --no-closure-search ./Hi_0_R2.TOnovel/junctions.bed ./Hi_0_R2.TOnovel/insertions.bed ./Hi_0_R2.TOnovel/deletions.bed ./Hi_0_R2.TOnovel/tmp/accepted_hits.sam ./Hi_0_R2.TOnovel/tmp/left_kept_reads.fq.candidate_hits.sam ./Hi_0_R2.TOnovel/tmp/left_kept_reads.fq
samtools view -S -b ./Hi_0_R2.TOnovel/tmp/accepted_hits.sam > ./Hi_0_R2.TOnovel/tmp/filerEHvoc
samtools sort ./Hi_0_R2.TOnovel/tmp/filerEHvoc ./Hi_0_R2.TOnovel/accepted_hits