/home/xianggan/bin/exoner/tophat --num-threads 4 --mate-inner-dist 38 --mate-std-dev 40 --max-multihits 10 --coverage-search --microexon-search -o ./Ler_0_R1.TOnovel ../novelgene.v2 ./Ler_0_R1.TOnovel/R38_L3_Ler_0_sdlg_R1_nss_barcode_TGC.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 ./Ler_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 ./Ler_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 ./Ler_0_R1.TOnovel/R38_L3_Ler_0_sdlg_R1_nss_barcode_TGC.unmap_1.flt_1.fq
bowtie -q --un ./Ler_0_R1.TOnovel/tmp/left_kept_reads_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 ../novelgene.v2 ./Ler_0_R1.TOnovel/tmp/left_kept_reads.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./Ler_0_R1.TOnovel/tmp/left_kept_reads.fq - > ./Ler_0_R1.TOnovel/tmp/fileDawvqE
/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 ./Ler_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 ./Ler_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 ./Ler_0_R1.TOnovel/tmp/left_kept_reads.fq /dev/null /dev/null /dev/null ./Ler_0_R1.TOnovel/tmp/left_kept_reads.bwtout  > ./Ler_0_R1.TOnovel/tmp/filejwSil7
bowtie -q --un ./Ler_0_R1.TOnovel/tmp/left_kept_reads_seg1_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 ../novelgene.v2 ./Ler_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 ./Ler_0_R1.TOnovel/tmp/left_kept_reads_seg1.fq - > ./Ler_0_R1.TOnovel/tmp/file0KslNT
bowtie -q --un ./Ler_0_R1.TOnovel/tmp/left_kept_reads_seg2_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 ../novelgene.v2 ./Ler_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 ./Ler_0_R1.TOnovel/tmp/left_kept_reads_seg2.fq - > ./Ler_0_R1.TOnovel/tmp/fileKqpiOK
bowtie -q --un ./Ler_0_R1.TOnovel/tmp/left_kept_reads_seg3_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 ../novelgene.v2 ./Ler_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 ./Ler_0_R1.TOnovel/tmp/left_kept_reads_seg3.fq - > ./Ler_0_R1.TOnovel/tmp/fileHaX2lG
/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 ./Ler_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 ./Ler_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 ./Ler_0_R1.TOnovel/tmp/left_kept_reads_seg1_missing.fq,./Ler_0_R1.TOnovel/tmp/left_kept_reads_seg2_missing.fq,./Ler_0_R1.TOnovel/tmp/left_kept_reads_seg3_missing.fq ../novelgene.v2.fa ./Ler_0_R1.TOnovel/tmp/segment.juncs ./Ler_0_R1.TOnovel/tmp/segment.insertions ./Ler_0_R1.TOnovel/tmp/segment.deletions ./Ler_0_R1.TOnovel/tmp/left_kept_reads.fq ./Ler_0_R1.TOnovel/tmp/left_kept_reads.bwtout ./Ler_0_R1.TOnovel/tmp/left_kept_reads_seg1.bwtout,./Ler_0_R1.TOnovel/tmp/left_kept_reads_seg2.bwtout,./Ler_0_R1.TOnovel/tmp/left_kept_reads_seg3.bwtout
/Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/juncs_db 3 25 ./Ler_0_R1.TOnovel/tmp/segment.juncs /dev/null /dev/null ../novelgene.v2.fa
bowtie-build ./Ler_0_R1.TOnovel/tmp/segment_juncs.fa ./Ler_0_R1.TOnovel/tmp/segment_juncs
bowtie -q -v 2 -p 4 -k 10 -m 10 ./Ler_0_R1.TOnovel/tmp/segment_juncs ./Ler_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 ./Ler_0_R1.TOnovel/tmp/left_kept_reads_seg1.fq - > ./Ler_0_R1.TOnovel/tmp/filep9Y9xf
bowtie -q -v 2 -p 4 -k 10 -m 10 ./Ler_0_R1.TOnovel/tmp/segment_juncs ./Ler_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 ./Ler_0_R1.TOnovel/tmp/left_kept_reads_seg2.fq - > ./Ler_0_R1.TOnovel/tmp/fileCuLu3Q
bowtie -q -v 2 -p 4 -k 10 -m 10 ./Ler_0_R1.TOnovel/tmp/segment_juncs ./Ler_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 ./Ler_0_R1.TOnovel/tmp/left_kept_reads_seg3.fq - > ./Ler_0_R1.TOnovel/tmp/filePtW5Vu
/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 ./Ler_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 ./Ler_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 ./Ler_0_R1.TOnovel/tmp/left_kept_reads.fq ./Ler_0_R1.TOnovel/tmp/segment.juncs /dev/null /dev/null ./Ler_0_R1.TOnovel/tmp/left_kept_reads_seg1.bwtout,./Ler_0_R1.TOnovel/tmp/left_kept_reads_seg2.bwtout,./Ler_0_R1.TOnovel/tmp/left_kept_reads_seg3.bwtout ./Ler_0_R1.TOnovel/tmp/left_kept_reads_seg1_to_spliced.bwtout,./Ler_0_R1.TOnovel/tmp/left_kept_reads_seg2_to_spliced.bwtout,./Ler_0_R1.TOnovel/tmp/left_kept_reads_seg3_to_spliced.bwtout > ./Ler_0_R1.TOnovel/tmp/left_kept_reads.fq.candidate_hits.sam
sort -k 1,1n --temporary-directory=./Ler_0_R1.TOnovel/tmp/ ./Ler_0_R1.TOnovel/tmp/filejwSil7 ./Ler_0_R1.TOnovel/tmp/left_kept_reads.fq.candidate_hits.sam > ./Ler_0_R1.TOnovel/tmp/filerDb2Jd
sort -k 1,1n --temporary-directory=./Ler_0_R1.TOnovel/tmp/ ./Ler_0_R1.TOnovel/tmp/filejwSil7 ./Ler_0_R1.TOnovel/tmp/left_kept_reads.fq.candidate_hits.sam
mv ./Ler_0_R1.TOnovel/tmp/filerDb2Jd ./Ler_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 ./Ler_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 ./Ler_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 ./Ler_0_R1.TOnovel/junctions.bed ./Ler_0_R1.TOnovel/insertions.bed ./Ler_0_R1.TOnovel/deletions.bed ./Ler_0_R1.TOnovel/tmp/accepted_hits.sam ./Ler_0_R1.TOnovel/tmp/left_kept_reads.fq.candidate_hits.sam ./Ler_0_R1.TOnovel/tmp/left_kept_reads.fq
samtools view -S -b ./Ler_0_R1.TOnovel/tmp/accepted_hits.sam > ./Ler_0_R1.TOnovel/tmp/filei4iapZ
samtools sort ./Ler_0_R1.TOnovel/tmp/filei4iapZ ./Ler_0_R1.TOnovel/accepted_hits