/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 Kn_0/ -G /data/www/arabcall/TAIR10_GFF3_genes_transposons.gff /data/arabidopsis/xiang/tair10_um Kn_0//Run33_lane3_Kn_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 Kn_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 Kn_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 Kn_0//Run33_lane3_Kn_0_seedling.fastq.flt_1.fq
bowtie -q --un Kn_0//tmp/left_kept_reads_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 /data/arabidopsis/xiang/tair10_um Kn_0//tmp/left_kept_reads.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Kn_0//tmp/left_kept_reads.fq - > Kn_0//tmp/file7dxPb7
/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 Kn_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 Kn_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 Kn_0//tmp/left_kept_reads.fq /dev/null /dev/null /dev/null Kn_0//tmp/left_kept_reads.bwtout  > Kn_0//tmp/fileVeTrxq
bowtie -q --un Kn_0//tmp/left_kept_reads_seg1_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 /data/arabidopsis/xiang/tair10_um Kn_0//tmp/left_kept_reads_seg1.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Kn_0//tmp/left_kept_reads_seg1.fq - > Kn_0//tmp/fileGoXHca
bowtie -q --un Kn_0//tmp/left_kept_reads_seg2_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 /data/arabidopsis/xiang/tair10_um Kn_0//tmp/left_kept_reads_seg2.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Kn_0//tmp/left_kept_reads_seg2.fq - > Kn_0//tmp/fileES2m0C
bowtie -q --un Kn_0//tmp/left_kept_reads_seg3_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 /data/arabidopsis/xiang/tair10_um Kn_0//tmp/left_kept_reads_seg3.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Kn_0//tmp/left_kept_reads_seg3.fq - > Kn_0//tmp/fileyXZPSK
/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 Kn_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 Kn_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 Kn_0//tmp/left_kept_reads_seg1_missing.fq,Kn_0//tmp/left_kept_reads_seg2_missing.fq,Kn_0//tmp/left_kept_reads_seg3_missing.fq /data/arabidopsis/xiang/tair10_um.fa Kn_0//tmp/segment.juncs Kn_0//tmp/segment.insertions Kn_0//tmp/segment.deletions Kn_0//tmp/left_kept_reads.fq Kn_0//tmp/left_kept_reads.bwtout Kn_0//tmp/left_kept_reads_seg1.bwtout,Kn_0//tmp/left_kept_reads_seg2.bwtout,Kn_0//tmp/left_kept_reads_seg3.bwtout
/Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/juncs_db 3 25 Kn_0//tmp/TAIR10_GFF3_genes_transposons.juncs,Kn_0//tmp/segment.juncs /dev/null /dev/null /data/arabidopsis/xiang/tair10_um.fa
bowtie-build Kn_0//tmp/segment_juncs.fa Kn_0//tmp/segment_juncs
bowtie -q -v 2 -p 4 -k 10 -m 10 Kn_0//tmp/segment_juncs Kn_0//tmp/left_kept_reads_seg1.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Kn_0//tmp/left_kept_reads_seg1.fq - > Kn_0//tmp/file8l7j2g
bowtie -q -v 2 -p 4 -k 10 -m 10 Kn_0//tmp/segment_juncs Kn_0//tmp/left_kept_reads_seg2.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Kn_0//tmp/left_kept_reads_seg2.fq - > Kn_0//tmp/files4GiV5
bowtie -q -v 2 -p 4 -k 10 -m 10 Kn_0//tmp/segment_juncs Kn_0//tmp/left_kept_reads_seg3.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Kn_0//tmp/left_kept_reads_seg3.fq - > Kn_0//tmp/file6FooBY
/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 Kn_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 Kn_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 Kn_0//tmp/left_kept_reads.fq Kn_0//tmp/TAIR10_GFF3_genes_transposons.juncs,Kn_0//tmp/segment.juncs /dev/null /dev/null Kn_0//tmp/left_kept_reads_seg1.bwtout,Kn_0//tmp/left_kept_reads_seg2.bwtout,Kn_0//tmp/left_kept_reads_seg3.bwtout Kn_0//tmp/left_kept_reads_seg1_to_spliced.bwtout,Kn_0//tmp/left_kept_reads_seg2_to_spliced.bwtout,Kn_0//tmp/left_kept_reads_seg3_to_spliced.bwtout > Kn_0//tmp/left_kept_reads.fq.candidate_hits.sam
sort -k 1,1n --temporary-directory=Kn_0//tmp/ Kn_0//tmp/fileVeTrxq Kn_0//tmp/left_kept_reads.fq.candidate_hits.sam > Kn_0//tmp/fileU94IYH
sort -k 1,1n --temporary-directory=Kn_0//tmp/ Kn_0//tmp/fileVeTrxq Kn_0//tmp/left_kept_reads.fq.candidate_hits.sam
mv Kn_0//tmp/fileU94IYH Kn_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 Kn_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 Kn_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 Kn_0//junctions.bed Kn_0//insertions.bed Kn_0//deletions.bed Kn_0//tmp/accepted_hits.sam Kn_0//tmp/left_kept_reads.fq.candidate_hits.sam Kn_0//tmp/left_kept_reads.fq
samtools view -S -b Kn_0//tmp/accepted_hits.sam > Kn_0//tmp/fileioquJn
samtools sort Kn_0//tmp/fileioquJn Kn_0//accepted_hits