/home/xianggan/bin/exoner/tophat --num-threads 4 --library-type fr-firststrand --mate-inner-dist 38 --mate-std-dev 40 --max-multihits 10 --coverage-search --microexon-search -o Tsu_0/ -G /Net/mus/data/www/arabcall/TAIR10_GFF3_genes_transposons.gff /Net/mus/data/arabidopsis/xiang/tair10_um Tsu_0//Run34_lane3_Tsu_0_seedling.flt_1.fq
/Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/gtf_juncs /Net/mus/data/www/arabcall/TAIR10_GFF3_genes_transposons.gff
/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 Tsu_0// --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 Tsu_0//tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 --gtf-annotations /Net/mus/data/www/arabcall/TAIR10_GFF3_genes_transposons.gff --library-type fr-firststrand --fastq Tsu_0//Run34_lane3_Tsu_0_seedling.flt_1.fq
bowtie -q --un Tsu_0//tmp/left_kept_reads_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 /Net/mus/data/arabidopsis/xiang/tair10_um Tsu_0//tmp/left_kept_reads.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Tsu_0//tmp/left_kept_reads.fq - > Tsu_0//tmp/file7e7EG5
/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 Tsu_0// --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 Tsu_0//tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 --gtf-annotations /Net/mus/data/www/arabcall/TAIR10_GFF3_genes_transposons.gff --library-type fr-firststrand /Net/mus/data/arabidopsis/xiang/tair10_um.fa Tsu_0//tmp/left_kept_reads.fq /dev/null /dev/null /dev/null Tsu_0//tmp/left_kept_reads.bwtout  > Tsu_0//tmp/fileUOOymJ
bowtie -q --un Tsu_0//tmp/left_kept_reads_seg1_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 /Net/mus/data/arabidopsis/xiang/tair10_um Tsu_0//tmp/left_kept_reads_seg1.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Tsu_0//tmp/left_kept_reads_seg1.fq - > Tsu_0//tmp/filemYKqMj
bowtie -q --un Tsu_0//tmp/left_kept_reads_seg2_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 /Net/mus/data/arabidopsis/xiang/tair10_um Tsu_0//tmp/left_kept_reads_seg2.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Tsu_0//tmp/left_kept_reads_seg2.fq - > Tsu_0//tmp/file6t96Qj
bowtie -q --un Tsu_0//tmp/left_kept_reads_seg3_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 /Net/mus/data/arabidopsis/xiang/tair10_um Tsu_0//tmp/left_kept_reads_seg3.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Tsu_0//tmp/left_kept_reads_seg3.fq - > Tsu_0//tmp/file8NmoPh
/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 Tsu_0// --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 Tsu_0//tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 --gtf-annotations /Net/mus/data/www/arabcall/TAIR10_GFF3_genes_transposons.gff --no-closure-search --library-type fr-firststrand --ium-reads Tsu_0//tmp/left_kept_reads_seg1_missing.fq,Tsu_0//tmp/left_kept_reads_seg2_missing.fq,Tsu_0//tmp/left_kept_reads_seg3_missing.fq /Net/mus/data/arabidopsis/xiang/tair10_um.fa Tsu_0//tmp/segment.juncs Tsu_0//tmp/segment.insertions Tsu_0//tmp/segment.deletions Tsu_0//tmp/left_kept_reads.fq Tsu_0//tmp/left_kept_reads.bwtout Tsu_0//tmp/left_kept_reads_seg1.bwtout,Tsu_0//tmp/left_kept_reads_seg2.bwtout,Tsu_0//tmp/left_kept_reads_seg3.bwtout
/Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/juncs_db 3 25 Tsu_0//tmp/TAIR10_GFF3_genes_transposons.juncs,Tsu_0//tmp/segment.juncs /dev/null /dev/null /Net/mus/data/arabidopsis/xiang/tair10_um.fa
bowtie-build Tsu_0//tmp/segment_juncs.fa Tsu_0//tmp/segment_juncs
bowtie -q -v 2 -p 4 -k 10 -m 10 Tsu_0//tmp/segment_juncs Tsu_0//tmp/left_kept_reads_seg1.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Tsu_0//tmp/left_kept_reads_seg1.fq - > Tsu_0//tmp/fileU7fCwo
bowtie -q -v 2 -p 4 -k 10 -m 10 Tsu_0//tmp/segment_juncs Tsu_0//tmp/left_kept_reads_seg2.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Tsu_0//tmp/left_kept_reads_seg2.fq - > Tsu_0//tmp/filetHRvmv
bowtie -q -v 2 -p 4 -k 10 -m 10 Tsu_0//tmp/segment_juncs Tsu_0//tmp/left_kept_reads_seg3.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Tsu_0//tmp/left_kept_reads_seg3.fq - > Tsu_0//tmp/fileH70nU9
/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 Tsu_0// --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 Tsu_0//tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 --gtf-annotations /Net/mus/data/www/arabcall/TAIR10_GFF3_genes_transposons.gff --no-closure-search --library-type fr-firststrand /Net/mus/data/arabidopsis/xiang/tair10_um.fa Tsu_0//tmp/left_kept_reads.fq Tsu_0//tmp/TAIR10_GFF3_genes_transposons.juncs,Tsu_0//tmp/segment.juncs /dev/null /dev/null Tsu_0//tmp/left_kept_reads_seg1.bwtout,Tsu_0//tmp/left_kept_reads_seg2.bwtout,Tsu_0//tmp/left_kept_reads_seg3.bwtout Tsu_0//tmp/left_kept_reads_seg1_to_spliced.bwtout,Tsu_0//tmp/left_kept_reads_seg2_to_spliced.bwtout,Tsu_0//tmp/left_kept_reads_seg3_to_spliced.bwtout > Tsu_0//tmp/left_kept_reads.fq.candidate_hits.sam
sort -k 1,1n --temporary-directory=Tsu_0//tmp/ Tsu_0//tmp/fileUOOymJ Tsu_0//tmp/left_kept_reads.fq.candidate_hits.sam > Tsu_0//tmp/file6c0prs
sort -k 1,1n --temporary-directory=Tsu_0//tmp/ Tsu_0//tmp/fileUOOymJ Tsu_0//tmp/left_kept_reads.fq.candidate_hits.sam
mv Tsu_0//tmp/file6c0prs Tsu_0//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 Tsu_0// --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 Tsu_0//tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 --gtf-annotations /Net/mus/data/www/arabcall/TAIR10_GFF3_genes_transposons.gff --no-closure-search --library-type fr-firststrand Tsu_0//junctions.bed Tsu_0//insertions.bed Tsu_0//deletions.bed Tsu_0//tmp/accepted_hits.sam Tsu_0//tmp/left_kept_reads.fq.candidate_hits.sam Tsu_0//tmp/left_kept_reads.fq
samtools view -S -b Tsu_0//tmp/accepted_hits.sam > Tsu_0//tmp/file19kIQN
samtools sort Tsu_0//tmp/file19kIQN Tsu_0//accepted_hits