/home/xianggan/bin/exoner/tophat --num-threads 4 --mate-inner-dist 38 --mate-std-dev 40 --max-multihits 10 --coverage-search --microexon-search -o Hi_0_R1/ -G /data/www/arabcall/TAIR10_GFF3_genes_transposons.gff /data/arabidopsis/xiang/tair10_um Hi_0_R1//R38_L3_Hi_0_sdlg_R1_nss_barcode_CAT.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 Hi_0_R1// --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 Hi_0_R1//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 --fastq Hi_0_R1//R38_L3_Hi_0_sdlg_R1_nss_barcode_CAT.flt_1.fq
bowtie -q --un Hi_0_R1//tmp/left_kept_reads_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 /data/arabidopsis/xiang/tair10_um Hi_0_R1//tmp/left_kept_reads.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Hi_0_R1//tmp/left_kept_reads.fq - > Hi_0_R1//tmp/file3kDd6D
/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 Hi_0_R1// --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 Hi_0_R1//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 /data/arabidopsis/xiang/tair10_um.fa Hi_0_R1//tmp/left_kept_reads.fq /dev/null /dev/null /dev/null Hi_0_R1//tmp/left_kept_reads.bwtout  > Hi_0_R1//tmp/file9V13kN
bowtie -q --un Hi_0_R1//tmp/left_kept_reads_seg1_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 /data/arabidopsis/xiang/tair10_um Hi_0_R1//tmp/left_kept_reads_seg1.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Hi_0_R1//tmp/left_kept_reads_seg1.fq - > Hi_0_R1//tmp/fileVGkrt0
bowtie -q --un Hi_0_R1//tmp/left_kept_reads_seg2_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 /data/arabidopsis/xiang/tair10_um Hi_0_R1//tmp/left_kept_reads_seg2.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Hi_0_R1//tmp/left_kept_reads_seg2.fq - > Hi_0_R1//tmp/file4zS7TP
bowtie -q --un Hi_0_R1//tmp/left_kept_reads_seg3_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 /data/arabidopsis/xiang/tair10_um Hi_0_R1//tmp/left_kept_reads_seg3.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Hi_0_R1//tmp/left_kept_reads_seg3.fq - > Hi_0_R1//tmp/fileGcANRn
/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 Hi_0_R1// --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 Hi_0_R1//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 --ium-reads Hi_0_R1//tmp/left_kept_reads_seg1_missing.fq,Hi_0_R1//tmp/left_kept_reads_seg2_missing.fq,Hi_0_R1//tmp/left_kept_reads_seg3_missing.fq /data/arabidopsis/xiang/tair10_um.fa Hi_0_R1//tmp/segment.juncs Hi_0_R1//tmp/segment.insertions Hi_0_R1//tmp/segment.deletions Hi_0_R1//tmp/left_kept_reads.fq Hi_0_R1//tmp/left_kept_reads.bwtout Hi_0_R1//tmp/left_kept_reads_seg1.bwtout,Hi_0_R1//tmp/left_kept_reads_seg2.bwtout,Hi_0_R1//tmp/left_kept_reads_seg3.bwtout
/Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/juncs_db 3 25 Hi_0_R1//tmp/TAIR10_GFF3_genes_transposons.juncs,Hi_0_R1//tmp/segment.juncs /dev/null /dev/null /data/arabidopsis/xiang/tair10_um.fa
bowtie-build Hi_0_R1//tmp/segment_juncs.fa Hi_0_R1//tmp/segment_juncs
bowtie -q -v 2 -p 4 -k 10 -m 10 Hi_0_R1//tmp/segment_juncs Hi_0_R1//tmp/left_kept_reads_seg1.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Hi_0_R1//tmp/left_kept_reads_seg1.fq - > Hi_0_R1//tmp/filed4greo
bowtie -q -v 2 -p 4 -k 10 -m 10 Hi_0_R1//tmp/segment_juncs Hi_0_R1//tmp/left_kept_reads_seg2.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Hi_0_R1//tmp/left_kept_reads_seg2.fq - > Hi_0_R1//tmp/filet2sNOf
bowtie -q -v 2 -p 4 -k 10 -m 10 Hi_0_R1//tmp/segment_juncs Hi_0_R1//tmp/left_kept_reads_seg3.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Hi_0_R1//tmp/left_kept_reads_seg3.fq - > Hi_0_R1//tmp/filek48ygk
/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 Hi_0_R1// --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 Hi_0_R1//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 /data/arabidopsis/xiang/tair10_um.fa Hi_0_R1//tmp/left_kept_reads.fq Hi_0_R1//tmp/TAIR10_GFF3_genes_transposons.juncs,Hi_0_R1//tmp/segment.juncs /dev/null /dev/null Hi_0_R1//tmp/left_kept_reads_seg1.bwtout,Hi_0_R1//tmp/left_kept_reads_seg2.bwtout,Hi_0_R1//tmp/left_kept_reads_seg3.bwtout Hi_0_R1//tmp/left_kept_reads_seg1_to_spliced.bwtout,Hi_0_R1//tmp/left_kept_reads_seg2_to_spliced.bwtout,Hi_0_R1//tmp/left_kept_reads_seg3_to_spliced.bwtout > Hi_0_R1//tmp/left_kept_reads.fq.candidate_hits.sam
sort -k 1,1n --temporary-directory=Hi_0_R1//tmp/ Hi_0_R1//tmp/file9V13kN Hi_0_R1//tmp/left_kept_reads.fq.candidate_hits.sam > Hi_0_R1//tmp/fileQXySET
sort -k 1,1n --temporary-directory=Hi_0_R1//tmp/ Hi_0_R1//tmp/file9V13kN Hi_0_R1//tmp/left_kept_reads.fq.candidate_hits.sam
mv Hi_0_R1//tmp/fileQXySET Hi_0_R1//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 Hi_0_R1// --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 Hi_0_R1//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 Hi_0_R1//junctions.bed Hi_0_R1//insertions.bed Hi_0_R1//deletions.bed Hi_0_R1//tmp/accepted_hits.sam Hi_0_R1//tmp/left_kept_reads.fq.candidate_hits.sam Hi_0_R1//tmp/left_kept_reads.fq
samtools view -S -b Hi_0_R1//tmp/accepted_hits.sam > Hi_0_R1//tmp/fileBpr8i1
samtools sort Hi_0_R1//tmp/fileBpr8i1 Hi_0_R1//accepted_hits