/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 Mt_0/ -G /data/www/arabcall/TAIR10_GFF3_genes_transposons.gff /data/arabidopsis/xiang/tair10_um Mt_0//Run32_lane6_Mt_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 Mt_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 Mt_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 Mt_0//Run32_lane6_Mt_0_seedling.fastq.flt_1.fq
bowtie -q --un Mt_0//tmp/left_kept_reads_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 /data/arabidopsis/xiang/tair10_um Mt_0//tmp/left_kept_reads.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Mt_0//tmp/left_kept_reads.fq - > Mt_0//tmp/filetBrXGv
/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 Mt_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 Mt_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 Mt_0//tmp/left_kept_reads.fq /dev/null /dev/null /dev/null Mt_0//tmp/left_kept_reads.bwtout  > Mt_0//tmp/fileX2JGFe
bowtie -q --un Mt_0//tmp/left_kept_reads_seg1_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 /data/arabidopsis/xiang/tair10_um Mt_0//tmp/left_kept_reads_seg1.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Mt_0//tmp/left_kept_reads_seg1.fq - > Mt_0//tmp/filee3QlP7
bowtie -q --un Mt_0//tmp/left_kept_reads_seg2_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 /data/arabidopsis/xiang/tair10_um Mt_0//tmp/left_kept_reads_seg2.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Mt_0//tmp/left_kept_reads_seg2.fq - > Mt_0//tmp/fileZSuuX6
bowtie -q --un Mt_0//tmp/left_kept_reads_seg3_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 /data/arabidopsis/xiang/tair10_um Mt_0//tmp/left_kept_reads_seg3.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Mt_0//tmp/left_kept_reads_seg3.fq - > Mt_0//tmp/file1OoVa4
/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 Mt_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 Mt_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 Mt_0//tmp/left_kept_reads_seg1_missing.fq,Mt_0//tmp/left_kept_reads_seg2_missing.fq,Mt_0//tmp/left_kept_reads_seg3_missing.fq /data/arabidopsis/xiang/tair10_um.fa Mt_0//tmp/segment.juncs Mt_0//tmp/segment.insertions Mt_0//tmp/segment.deletions Mt_0//tmp/left_kept_reads.fq Mt_0//tmp/left_kept_reads.bwtout Mt_0//tmp/left_kept_reads_seg1.bwtout,Mt_0//tmp/left_kept_reads_seg2.bwtout,Mt_0//tmp/left_kept_reads_seg3.bwtout
/Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/juncs_db 3 25 Mt_0//tmp/TAIR10_GFF3_genes_transposons.juncs,Mt_0//tmp/segment.juncs /dev/null /dev/null /data/arabidopsis/xiang/tair10_um.fa
bowtie-build Mt_0//tmp/segment_juncs.fa Mt_0//tmp/segment_juncs
bowtie -q -v 2 -p 4 -k 10 -m 10 Mt_0//tmp/segment_juncs Mt_0//tmp/left_kept_reads_seg1.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Mt_0//tmp/left_kept_reads_seg1.fq - > Mt_0//tmp/file8k0U2m
bowtie -q -v 2 -p 4 -k 10 -m 10 Mt_0//tmp/segment_juncs Mt_0//tmp/left_kept_reads_seg2.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Mt_0//tmp/left_kept_reads_seg2.fq - > Mt_0//tmp/file29DgrM
bowtie -q -v 2 -p 4 -k 10 -m 10 Mt_0//tmp/segment_juncs Mt_0//tmp/left_kept_reads_seg3.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Mt_0//tmp/left_kept_reads_seg3.fq - > Mt_0//tmp/filem5vIYz
/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 Mt_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 Mt_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 Mt_0//tmp/left_kept_reads.fq Mt_0//tmp/TAIR10_GFF3_genes_transposons.juncs,Mt_0//tmp/segment.juncs /dev/null /dev/null Mt_0//tmp/left_kept_reads_seg1.bwtout,Mt_0//tmp/left_kept_reads_seg2.bwtout,Mt_0//tmp/left_kept_reads_seg3.bwtout Mt_0//tmp/left_kept_reads_seg1_to_spliced.bwtout,Mt_0//tmp/left_kept_reads_seg2_to_spliced.bwtout,Mt_0//tmp/left_kept_reads_seg3_to_spliced.bwtout > Mt_0//tmp/left_kept_reads.fq.candidate_hits.sam
sort -k 1,1n --temporary-directory=Mt_0//tmp/ Mt_0//tmp/fileX2JGFe Mt_0//tmp/left_kept_reads.fq.candidate_hits.sam > Mt_0//tmp/filegOQnea
sort -k 1,1n --temporary-directory=Mt_0//tmp/ Mt_0//tmp/fileX2JGFe Mt_0//tmp/left_kept_reads.fq.candidate_hits.sam
mv Mt_0//tmp/filegOQnea Mt_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 Mt_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 Mt_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 Mt_0//junctions.bed Mt_0//insertions.bed Mt_0//deletions.bed Mt_0//tmp/accepted_hits.sam Mt_0//tmp/left_kept_reads.fq.candidate_hits.sam Mt_0//tmp/left_kept_reads.fq
samtools view -S -b Mt_0//tmp/accepted_hits.sam > Mt_0//tmp/file4u6vqP
samtools sort Mt_0//tmp/file4u6vqP Mt_0//accepted_hits