/home/xianggan/bin/exoner/tophat --num-threads 4 --mate-inner-dist 38 --mate-std-dev 40 --max-multihits 10 --coverage-search --microexon-search -o Col_0_R2/ -G /data/www/arabcall/TAIR10_GFF3_genes_transposons.gff /data/arabidopsis/xiang/tair10_um Col_0_R2//R38_L2_Col_0_sdlg_R2_nss_barcode_GTA.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 Col_0_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 Col_0_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 Col_0_R2//R38_L2_Col_0_sdlg_R2_nss_barcode_GTA.flt_1.fq
bowtie -q --un Col_0_R2//tmp/left_kept_reads_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 /data/arabidopsis/xiang/tair10_um Col_0_R2//tmp/left_kept_reads.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Col_0_R2//tmp/left_kept_reads.fq - > Col_0_R2//tmp/fileyPSXOh
/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 Col_0_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 Col_0_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 Col_0_R2//tmp/left_kept_reads.fq /dev/null /dev/null /dev/null Col_0_R2//tmp/left_kept_reads.bwtout  > Col_0_R2//tmp/filesKumae
bowtie -q --un Col_0_R2//tmp/left_kept_reads_seg1_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 /data/arabidopsis/xiang/tair10_um Col_0_R2//tmp/left_kept_reads_seg1.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Col_0_R2//tmp/left_kept_reads_seg1.fq - > Col_0_R2//tmp/filerb4Y0q
bowtie -q --un Col_0_R2//tmp/left_kept_reads_seg2_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 /data/arabidopsis/xiang/tair10_um Col_0_R2//tmp/left_kept_reads_seg2.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Col_0_R2//tmp/left_kept_reads_seg2.fq - > Col_0_R2//tmp/fileDc2Vr6
bowtie -q --un Col_0_R2//tmp/left_kept_reads_seg3_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 /data/arabidopsis/xiang/tair10_um Col_0_R2//tmp/left_kept_reads_seg3.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Col_0_R2//tmp/left_kept_reads_seg3.fq - > Col_0_R2//tmp/file5lLbf9
/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 Col_0_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 Col_0_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 Col_0_R2//tmp/left_kept_reads_seg1_missing.fq,Col_0_R2//tmp/left_kept_reads_seg2_missing.fq,Col_0_R2//tmp/left_kept_reads_seg3_missing.fq /data/arabidopsis/xiang/tair10_um.fa Col_0_R2//tmp/segment.juncs Col_0_R2//tmp/segment.insertions Col_0_R2//tmp/segment.deletions Col_0_R2//tmp/left_kept_reads.fq Col_0_R2//tmp/left_kept_reads.bwtout Col_0_R2//tmp/left_kept_reads_seg1.bwtout,Col_0_R2//tmp/left_kept_reads_seg2.bwtout,Col_0_R2//tmp/left_kept_reads_seg3.bwtout
/Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/juncs_db 3 25 Col_0_R2//tmp/TAIR10_GFF3_genes_transposons.juncs,Col_0_R2//tmp/segment.juncs /dev/null /dev/null /data/arabidopsis/xiang/tair10_um.fa
bowtie-build Col_0_R2//tmp/segment_juncs.fa Col_0_R2//tmp/segment_juncs
bowtie -q -v 2 -p 4 -k 10 -m 10 Col_0_R2//tmp/segment_juncs Col_0_R2//tmp/left_kept_reads_seg1.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Col_0_R2//tmp/left_kept_reads_seg1.fq - > Col_0_R2//tmp/fileTubvRf
bowtie -q -v 2 -p 4 -k 10 -m 10 Col_0_R2//tmp/segment_juncs Col_0_R2//tmp/left_kept_reads_seg2.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Col_0_R2//tmp/left_kept_reads_seg2.fq - > Col_0_R2//tmp/file6OWwtX
bowtie -q -v 2 -p 4 -k 10 -m 10 Col_0_R2//tmp/segment_juncs Col_0_R2//tmp/left_kept_reads_seg3.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Col_0_R2//tmp/left_kept_reads_seg3.fq - > Col_0_R2//tmp/filempArkA
/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 Col_0_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 Col_0_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 Col_0_R2//tmp/left_kept_reads.fq Col_0_R2//tmp/TAIR10_GFF3_genes_transposons.juncs,Col_0_R2//tmp/segment.juncs /dev/null /dev/null Col_0_R2//tmp/left_kept_reads_seg1.bwtout,Col_0_R2//tmp/left_kept_reads_seg2.bwtout,Col_0_R2//tmp/left_kept_reads_seg3.bwtout Col_0_R2//tmp/left_kept_reads_seg1_to_spliced.bwtout,Col_0_R2//tmp/left_kept_reads_seg2_to_spliced.bwtout,Col_0_R2//tmp/left_kept_reads_seg3_to_spliced.bwtout > Col_0_R2//tmp/left_kept_reads.fq.candidate_hits.sam
sort -k 1,1n --temporary-directory=Col_0_R2//tmp/ Col_0_R2//tmp/filesKumae Col_0_R2//tmp/left_kept_reads.fq.candidate_hits.sam > Col_0_R2//tmp/filelJqjNb
sort -k 1,1n --temporary-directory=Col_0_R2//tmp/ Col_0_R2//tmp/filesKumae Col_0_R2//tmp/left_kept_reads.fq.candidate_hits.sam
mv Col_0_R2//tmp/filelJqjNb Col_0_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 Col_0_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 Col_0_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 Col_0_R2//junctions.bed Col_0_R2//insertions.bed Col_0_R2//deletions.bed Col_0_R2//tmp/accepted_hits.sam Col_0_R2//tmp/left_kept_reads.fq.candidate_hits.sam Col_0_R2//tmp/left_kept_reads.fq
samtools view -S -b Col_0_R2//tmp/accepted_hits.sam > Col_0_R2//tmp/fileOX8dl6
samtools sort Col_0_R2//tmp/fileOX8dl6 Col_0_R2//accepted_hits