/home/xianggan/bin/exoner/tophat --num-threads 4 --mate-inner-dist 38 --mate-std-dev 40 --max-multihits 10 --coverage-search --microexon-search -o ./wil_2 wil_2.novel ./wil_2/acc18_unmap.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 ./wil_2/ --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 ./wil_2/tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 --fastq ./wil_2/acc18_unmap.flt_1.fq
bowtie -q --un ./wil_2/tmp/left_kept_reads_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 wil_2.novel ./wil_2/tmp/left_kept_reads.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./wil_2/tmp/left_kept_reads.fq - > ./wil_2/tmp/fileqon57U
/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 ./wil_2/ --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 ./wil_2/tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 wil_2.novel.fa ./wil_2/tmp/left_kept_reads.fq /dev/null /dev/null /dev/null ./wil_2/tmp/left_kept_reads.bwtout  > ./wil_2/tmp/fileCovnBN
bowtie -q --un ./wil_2/tmp/left_kept_reads_seg1_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 wil_2.novel ./wil_2/tmp/left_kept_reads_seg1.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./wil_2/tmp/left_kept_reads_seg1.fq - > ./wil_2/tmp/filesKGXbH
bowtie -q --un ./wil_2/tmp/left_kept_reads_seg2_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 wil_2.novel ./wil_2/tmp/left_kept_reads_seg2.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./wil_2/tmp/left_kept_reads_seg2.fq - > ./wil_2/tmp/fileRTlROR
bowtie -q --un ./wil_2/tmp/left_kept_reads_seg3_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 wil_2.novel ./wil_2/tmp/left_kept_reads_seg3.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./wil_2/tmp/left_kept_reads_seg3.fq - > ./wil_2/tmp/fileVEZifk
/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 ./wil_2/ --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 ./wil_2/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 ./wil_2/tmp/left_kept_reads_seg1_missing.fq,./wil_2/tmp/left_kept_reads_seg2_missing.fq,./wil_2/tmp/left_kept_reads_seg3_missing.fq wil_2.novel.fa ./wil_2/tmp/segment.juncs ./wil_2/tmp/segment.insertions ./wil_2/tmp/segment.deletions ./wil_2/tmp/left_kept_reads.fq ./wil_2/tmp/left_kept_reads.bwtout ./wil_2/tmp/left_kept_reads_seg1.bwtout,./wil_2/tmp/left_kept_reads_seg2.bwtout,./wil_2/tmp/left_kept_reads_seg3.bwtout
/Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/juncs_db 3 25 ./wil_2/tmp/segment.juncs /dev/null /dev/null wil_2.novel.fa
bowtie-build ./wil_2/tmp/segment_juncs.fa ./wil_2/tmp/segment_juncs
bowtie -q -v 2 -p 4 -k 10 -m 10 ./wil_2/tmp/segment_juncs ./wil_2/tmp/left_kept_reads_seg1.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./wil_2/tmp/left_kept_reads_seg1.fq - > ./wil_2/tmp/filet74ivp
bowtie -q -v 2 -p 4 -k 10 -m 10 ./wil_2/tmp/segment_juncs ./wil_2/tmp/left_kept_reads_seg2.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./wil_2/tmp/left_kept_reads_seg2.fq - > ./wil_2/tmp/filert9Se2
bowtie -q -v 2 -p 4 -k 10 -m 10 ./wil_2/tmp/segment_juncs ./wil_2/tmp/left_kept_reads_seg3.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq ./wil_2/tmp/left_kept_reads_seg3.fq - > ./wil_2/tmp/fileN0DkMm
/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 ./wil_2/ --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 ./wil_2/tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 --no-closure-search wil_2.novel.fa ./wil_2/tmp/left_kept_reads.fq ./wil_2/tmp/segment.juncs /dev/null /dev/null ./wil_2/tmp/left_kept_reads_seg1.bwtout,./wil_2/tmp/left_kept_reads_seg2.bwtout,./wil_2/tmp/left_kept_reads_seg3.bwtout ./wil_2/tmp/left_kept_reads_seg1_to_spliced.bwtout,./wil_2/tmp/left_kept_reads_seg2_to_spliced.bwtout,./wil_2/tmp/left_kept_reads_seg3_to_spliced.bwtout > ./wil_2/tmp/left_kept_reads.fq.candidate_hits.sam
sort -k 1,1n --temporary-directory=./wil_2/tmp/ ./wil_2/tmp/fileCovnBN ./wil_2/tmp/left_kept_reads.fq.candidate_hits.sam > ./wil_2/tmp/fileS7wv0l
sort -k 1,1n --temporary-directory=./wil_2/tmp/ ./wil_2/tmp/fileCovnBN ./wil_2/tmp/left_kept_reads.fq.candidate_hits.sam
mv ./wil_2/tmp/fileS7wv0l ./wil_2/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 ./wil_2/ --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 ./wil_2/tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 --no-closure-search ./wil_2/junctions.bed ./wil_2/insertions.bed ./wil_2/deletions.bed ./wil_2/tmp/accepted_hits.sam ./wil_2/tmp/left_kept_reads.fq.candidate_hits.sam ./wil_2/tmp/left_kept_reads.fq
samtools view -S -b ./wil_2/tmp/accepted_hits.sam > ./wil_2/tmp/fileheOONF
samtools sort ./wil_2/tmp/fileheOONF ./wil_2/accepted_hits