/home/xianggan/bin/exoner/tophat --num-threads 4 --mate-inner-dist 38 --mate-std-dev 40 --max-multihits 10 --coverage-search --microexon-search -o A_lyr_R2/ -G /data/www/arabcall/TAIR10_GFF3_genes_transposons.gff /data/arabidopsis/xiang/tair10_um A_lyr_R2//R39_L4_A_lyr_sdlg_R2_nss_barcode_ACG.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 A_lyr_R2// --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 A_lyr_R2//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 A_lyr_R2//R39_L4_A_lyr_sdlg_R2_nss_barcode_ACG.flt_1.fq
bowtie -q --un A_lyr_R2//tmp/left_kept_reads_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 /data/arabidopsis/xiang/tair10_um A_lyr_R2//tmp/left_kept_reads.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq A_lyr_R2//tmp/left_kept_reads.fq - > A_lyr_R2//tmp/file5jtV7E
/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 A_lyr_R2// --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 A_lyr_R2//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 A_lyr_R2//tmp/left_kept_reads.fq /dev/null /dev/null /dev/null A_lyr_R2//tmp/left_kept_reads.bwtout  > A_lyr_R2//tmp/file3mqaoJ
bowtie -q --un A_lyr_R2//tmp/left_kept_reads_seg1_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 /data/arabidopsis/xiang/tair10_um A_lyr_R2//tmp/left_kept_reads_seg1.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq A_lyr_R2//tmp/left_kept_reads_seg1.fq - > A_lyr_R2//tmp/fileBBHjLx
bowtie -q --un A_lyr_R2//tmp/left_kept_reads_seg2_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 /data/arabidopsis/xiang/tair10_um A_lyr_R2//tmp/left_kept_reads_seg2.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq A_lyr_R2//tmp/left_kept_reads_seg2.fq - > A_lyr_R2//tmp/fileGKTk1U
bowtie -q --un A_lyr_R2//tmp/left_kept_reads_seg3_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 /data/arabidopsis/xiang/tair10_um A_lyr_R2//tmp/left_kept_reads_seg3.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq A_lyr_R2//tmp/left_kept_reads_seg3.fq - > A_lyr_R2//tmp/fileAWIjVc
/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 A_lyr_R2// --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 A_lyr_R2//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 A_lyr_R2//tmp/left_kept_reads_seg1_missing.fq,A_lyr_R2//tmp/left_kept_reads_seg2_missing.fq,A_lyr_R2//tmp/left_kept_reads_seg3_missing.fq /data/arabidopsis/xiang/tair10_um.fa A_lyr_R2//tmp/segment.juncs A_lyr_R2//tmp/segment.insertions A_lyr_R2//tmp/segment.deletions A_lyr_R2//tmp/left_kept_reads.fq A_lyr_R2//tmp/left_kept_reads.bwtout A_lyr_R2//tmp/left_kept_reads_seg1.bwtout,A_lyr_R2//tmp/left_kept_reads_seg2.bwtout,A_lyr_R2//tmp/left_kept_reads_seg3.bwtout
/Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/juncs_db 3 25 A_lyr_R2//tmp/TAIR10_GFF3_genes_transposons.juncs,A_lyr_R2//tmp/segment.juncs /dev/null /dev/null /data/arabidopsis/xiang/tair10_um.fa
bowtie-build A_lyr_R2//tmp/segment_juncs.fa A_lyr_R2//tmp/segment_juncs
bowtie -q -v 2 -p 4 -k 10 -m 10 A_lyr_R2//tmp/segment_juncs A_lyr_R2//tmp/left_kept_reads_seg1.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq A_lyr_R2//tmp/left_kept_reads_seg1.fq - > A_lyr_R2//tmp/filekJqNL6
bowtie -q -v 2 -p 4 -k 10 -m 10 A_lyr_R2//tmp/segment_juncs A_lyr_R2//tmp/left_kept_reads_seg2.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq A_lyr_R2//tmp/left_kept_reads_seg2.fq - > A_lyr_R2//tmp/fileq0sEow
bowtie -q -v 2 -p 4 -k 10 -m 10 A_lyr_R2//tmp/segment_juncs A_lyr_R2//tmp/left_kept_reads_seg3.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq A_lyr_R2//tmp/left_kept_reads_seg3.fq - > A_lyr_R2//tmp/fileAPSlSd
/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 A_lyr_R2// --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 A_lyr_R2//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 A_lyr_R2//tmp/left_kept_reads.fq A_lyr_R2//tmp/TAIR10_GFF3_genes_transposons.juncs,A_lyr_R2//tmp/segment.juncs /dev/null /dev/null A_lyr_R2//tmp/left_kept_reads_seg1.bwtout,A_lyr_R2//tmp/left_kept_reads_seg2.bwtout,A_lyr_R2//tmp/left_kept_reads_seg3.bwtout A_lyr_R2//tmp/left_kept_reads_seg1_to_spliced.bwtout,A_lyr_R2//tmp/left_kept_reads_seg2_to_spliced.bwtout,A_lyr_R2//tmp/left_kept_reads_seg3_to_spliced.bwtout > A_lyr_R2//tmp/left_kept_reads.fq.candidate_hits.sam
sort -k 1,1n --temporary-directory=A_lyr_R2//tmp/ A_lyr_R2//tmp/file3mqaoJ A_lyr_R2//tmp/left_kept_reads.fq.candidate_hits.sam > A_lyr_R2//tmp/fileajkYAF
sort -k 1,1n --temporary-directory=A_lyr_R2//tmp/ A_lyr_R2//tmp/file3mqaoJ A_lyr_R2//tmp/left_kept_reads.fq.candidate_hits.sam
mv A_lyr_R2//tmp/fileajkYAF A_lyr_R2//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 A_lyr_R2// --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 A_lyr_R2//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 A_lyr_R2//junctions.bed A_lyr_R2//insertions.bed A_lyr_R2//deletions.bed A_lyr_R2//tmp/accepted_hits.sam A_lyr_R2//tmp/left_kept_reads.fq.candidate_hits.sam A_lyr_R2//tmp/left_kept_reads.fq
samtools view -S -b A_lyr_R2//tmp/accepted_hits.sam > A_lyr_R2//tmp/filePkjHOB
samtools sort A_lyr_R2//tmp/filePkjHOB A_lyr_R2//accepted_hits