/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 Ler_0/ -G /data/www/arabcall/TAIR10_GFF3_genes_transposons.gff /data/arabidopsis/xiang/tair10_um Ler_0//Run33_lane4_Ler_0_seedling.fastq.flt_1.fq
/Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/gtf_juncs /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 Ler_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 Ler_0//tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 --gtf-annotations /data/www/arabcall/TAIR10_GFF3_genes_transposons.gff --library-type fr-firststrand --fastq Ler_0//Run33_lane4_Ler_0_seedling.fastq.flt_1.fq
bowtie -q --un Ler_0//tmp/left_kept_reads_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 /data/arabidopsis/xiang/tair10_um Ler_0//tmp/left_kept_reads.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Ler_0//tmp/left_kept_reads.fq - > Ler_0//tmp/fileAW4hB6
/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// --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//tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 --gtf-annotations /data/www/arabcall/TAIR10_GFF3_genes_transposons.gff --library-type fr-firststrand /data/arabidopsis/xiang/tair10_um.fa Ler_0//tmp/left_kept_reads.fq /dev/null /dev/null /dev/null Ler_0//tmp/left_kept_reads.bwtout  > Ler_0//tmp/file5bExEO
bowtie -q --un Ler_0//tmp/left_kept_reads_seg1_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 /data/arabidopsis/xiang/tair10_um Ler_0//tmp/left_kept_reads_seg1.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Ler_0//tmp/left_kept_reads_seg1.fq - > Ler_0//tmp/fileUNya8C
bowtie -q --un Ler_0//tmp/left_kept_reads_seg2_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 /data/arabidopsis/xiang/tair10_um Ler_0//tmp/left_kept_reads_seg2.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Ler_0//tmp/left_kept_reads_seg2.fq - > Ler_0//tmp/fileRGIQ11
bowtie -q --un Ler_0//tmp/left_kept_reads_seg3_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 /data/arabidopsis/xiang/tair10_um Ler_0//tmp/left_kept_reads_seg3.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Ler_0//tmp/left_kept_reads_seg3.fq - > Ler_0//tmp/filewzA4b0
/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// --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//tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 --gtf-annotations /data/www/arabcall/TAIR10_GFF3_genes_transposons.gff --no-closure-search --library-type fr-firststrand --ium-reads Ler_0//tmp/left_kept_reads_seg1_missing.fq,Ler_0//tmp/left_kept_reads_seg2_missing.fq,Ler_0//tmp/left_kept_reads_seg3_missing.fq /data/arabidopsis/xiang/tair10_um.fa Ler_0//tmp/segment.juncs Ler_0//tmp/segment.insertions Ler_0//tmp/segment.deletions Ler_0//tmp/left_kept_reads.fq Ler_0//tmp/left_kept_reads.bwtout Ler_0//tmp/left_kept_reads_seg1.bwtout,Ler_0//tmp/left_kept_reads_seg2.bwtout,Ler_0//tmp/left_kept_reads_seg3.bwtout
/Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/juncs_db 3 25 Ler_0//tmp/TAIR10_GFF3_genes_transposons.juncs,Ler_0//tmp/segment.juncs /dev/null /dev/null /data/arabidopsis/xiang/tair10_um.fa
bowtie-build Ler_0//tmp/segment_juncs.fa Ler_0//tmp/segment_juncs
bowtie -q -v 2 -p 4 -k 10 -m 10 Ler_0//tmp/segment_juncs Ler_0//tmp/left_kept_reads_seg1.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Ler_0//tmp/left_kept_reads_seg1.fq - > Ler_0//tmp/filenbbGeJ
bowtie -q -v 2 -p 4 -k 10 -m 10 Ler_0//tmp/segment_juncs Ler_0//tmp/left_kept_reads_seg2.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Ler_0//tmp/left_kept_reads_seg2.fq - > Ler_0//tmp/fileEiwKHm
bowtie -q -v 2 -p 4 -k 10 -m 10 Ler_0//tmp/segment_juncs Ler_0//tmp/left_kept_reads_seg3.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Ler_0//tmp/left_kept_reads_seg3.fq - > Ler_0//tmp/filea84wTN
/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// --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//tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 --gtf-annotations /data/www/arabcall/TAIR10_GFF3_genes_transposons.gff --no-closure-search --library-type fr-firststrand /data/arabidopsis/xiang/tair10_um.fa Ler_0//tmp/left_kept_reads.fq Ler_0//tmp/TAIR10_GFF3_genes_transposons.juncs,Ler_0//tmp/segment.juncs /dev/null /dev/null Ler_0//tmp/left_kept_reads_seg1.bwtout,Ler_0//tmp/left_kept_reads_seg2.bwtout,Ler_0//tmp/left_kept_reads_seg3.bwtout Ler_0//tmp/left_kept_reads_seg1_to_spliced.bwtout,Ler_0//tmp/left_kept_reads_seg2_to_spliced.bwtout,Ler_0//tmp/left_kept_reads_seg3_to_spliced.bwtout > Ler_0//tmp/left_kept_reads.fq.candidate_hits.sam
sort -k 1,1n --temporary-directory=Ler_0//tmp/ Ler_0//tmp/file5bExEO Ler_0//tmp/left_kept_reads.fq.candidate_hits.sam > Ler_0//tmp/fileBJV1m1
sort -k 1,1n --temporary-directory=Ler_0//tmp/ Ler_0//tmp/file5bExEO Ler_0//tmp/left_kept_reads.fq.candidate_hits.sam
mv Ler_0//tmp/fileBJV1m1 Ler_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 Ler_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 Ler_0//tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 --inner-dist-mean 38 --inner-dist-std-dev 40 --gtf-annotations /data/www/arabcall/TAIR10_GFF3_genes_transposons.gff --no-closure-search --library-type fr-firststrand Ler_0//junctions.bed Ler_0//insertions.bed Ler_0//deletions.bed Ler_0//tmp/accepted_hits.sam Ler_0//tmp/left_kept_reads.fq.candidate_hits.sam Ler_0//tmp/left_kept_reads.fq
samtools view -S -b Ler_0//tmp/accepted_hits.sam > Ler_0//tmp/fileOLnGpj
samtools sort Ler_0//tmp/fileOLnGpj Ler_0//accepted_hits