/home/xianggan/bin/exoner/tophat --num-threads 4 --mate-inner-dist 38 --mate-std-dev 40 --max-multihits 10 --coverage-search --microexon-search -o ./Col_0_R1.TOnovel ../novelgene.v2 ./Col_0_R1.TOnovel/R38_L1_Col_0_sdlg_R1_nss_barcode_GTA.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 ./Col_0_R1.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 ./Col_0_R1.TOnovel/tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 --fastq ./Col_0_R1.TOnovel/R38_L1_Col_0_sdlg_R1_nss_barcode_GTA.unmap_1.flt_1.fq
bowtie -q --un ./Col_0_R1.TOnovel/tmp/left_kept_reads_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 ../novelgene.v2 ./Col_0_R1.TOnovel/tmp/left_kept_reads.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./Col_0_R1.TOnovel/tmp/left_kept_reads.fq - > ./Col_0_R1.TOnovel/tmp/filetNpgyT
/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 ./Col_0_R1.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 ./Col_0_R1.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 ./Col_0_R1.TOnovel/tmp/left_kept_reads.fq /dev/null /dev/null /dev/null ./Col_0_R1.TOnovel/tmp/left_kept_reads.bwtout  > ./Col_0_R1.TOnovel/tmp/fileGMxxHi
bowtie -q --un ./Col_0_R1.TOnovel/tmp/left_kept_reads_seg1_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 ../novelgene.v2 ./Col_0_R1.TOnovel/tmp/left_kept_reads_seg1.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./Col_0_R1.TOnovel/tmp/left_kept_reads_seg1.fq - > ./Col_0_R1.TOnovel/tmp/fileipy222
bowtie -q --un ./Col_0_R1.TOnovel/tmp/left_kept_reads_seg2_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 ../novelgene.v2 ./Col_0_R1.TOnovel/tmp/left_kept_reads_seg2.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./Col_0_R1.TOnovel/tmp/left_kept_reads_seg2.fq - > ./Col_0_R1.TOnovel/tmp/filecsKllS
bowtie -q --un ./Col_0_R1.TOnovel/tmp/left_kept_reads_seg3_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 ../novelgene.v2 ./Col_0_R1.TOnovel/tmp/left_kept_reads_seg3.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./Col_0_R1.TOnovel/tmp/left_kept_reads_seg3.fq - > ./Col_0_R1.TOnovel/tmp/file0sCfBM
/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 ./Col_0_R1.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 ./Col_0_R1.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 ./Col_0_R1.TOnovel/tmp/left_kept_reads_seg1_missing.fq,./Col_0_R1.TOnovel/tmp/left_kept_reads_seg2_missing.fq,./Col_0_R1.TOnovel/tmp/left_kept_reads_seg3_missing.fq ../novelgene.v2.fa ./Col_0_R1.TOnovel/tmp/segment.juncs ./Col_0_R1.TOnovel/tmp/segment.insertions ./Col_0_R1.TOnovel/tmp/segment.deletions ./Col_0_R1.TOnovel/tmp/left_kept_reads.fq ./Col_0_R1.TOnovel/tmp/left_kept_reads.bwtout ./Col_0_R1.TOnovel/tmp/left_kept_reads_seg1.bwtout,./Col_0_R1.TOnovel/tmp/left_kept_reads_seg2.bwtout,./Col_0_R1.TOnovel/tmp/left_kept_reads_seg3.bwtout
/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 ./Col_0_R1.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 ./Col_0_R1.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 ./Col_0_R1.TOnovel/tmp/left_kept_reads.fq /dev/null /dev/null /dev/null ./Col_0_R1.TOnovel/tmp/left_kept_reads_seg1.bwtout,./Col_0_R1.TOnovel/tmp/left_kept_reads_seg2.bwtout,./Col_0_R1.TOnovel/tmp/left_kept_reads_seg3.bwtout  > ./Col_0_R1.TOnovel/tmp/left_kept_reads.fq.candidate_hits.sam
sort -k 1,1n --temporary-directory=./Col_0_R1.TOnovel/tmp/ ./Col_0_R1.TOnovel/tmp/fileGMxxHi ./Col_0_R1.TOnovel/tmp/left_kept_reads.fq.candidate_hits.sam > ./Col_0_R1.TOnovel/tmp/fileAgg2tg
sort -k 1,1n --temporary-directory=./Col_0_R1.TOnovel/tmp/ ./Col_0_R1.TOnovel/tmp/fileGMxxHi ./Col_0_R1.TOnovel/tmp/left_kept_reads.fq.candidate_hits.sam
mv ./Col_0_R1.TOnovel/tmp/fileAgg2tg ./Col_0_R1.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 ./Col_0_R1.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 ./Col_0_R1.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 ./Col_0_R1.TOnovel/junctions.bed ./Col_0_R1.TOnovel/insertions.bed ./Col_0_R1.TOnovel/deletions.bed ./Col_0_R1.TOnovel/tmp/accepted_hits.sam ./Col_0_R1.TOnovel/tmp/left_kept_reads.fq.candidate_hits.sam ./Col_0_R1.TOnovel/tmp/left_kept_reads.fq
samtools view -S -b ./Col_0_R1.TOnovel/tmp/accepted_hits.sam > ./Col_0_R1.TOnovel/tmp/fileuwtuaN
samtools sort ./Col_0_R1.TOnovel/tmp/fileuwtuaN ./Col_0_R1.TOnovel/accepted_hits