/home/xianggan/bin/exoner/tophat --num-threads 4 --mate-inner-dist 38 --mate-std-dev 40 --max-multihits 10 --coverage-search --microexon-search -o Ct_1_R1/ -G /data/www/arabcall/TAIR10_GFF3_genes_transposons.gff /data/arabidopsis/xiang/tair10_um Ct_1_R1//R38_L1_Ct_1_sdlg_R1_nss_barcode_TGC.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 Ct_1_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 Ct_1_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 Ct_1_R1//R38_L1_Ct_1_sdlg_R1_nss_barcode_TGC.flt_1.fq
bowtie -q --un Ct_1_R1//tmp/left_kept_reads_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 /data/arabidopsis/xiang/tair10_um Ct_1_R1//tmp/left_kept_reads.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Ct_1_R1//tmp/left_kept_reads.fq - > Ct_1_R1//tmp/filemL8uMP
/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 Ct_1_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 Ct_1_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 Ct_1_R1//tmp/left_kept_reads.fq /dev/null /dev/null /dev/null Ct_1_R1//tmp/left_kept_reads.bwtout  > Ct_1_R1//tmp/fileQP7jq7
bowtie -q --un Ct_1_R1//tmp/left_kept_reads_seg1_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 /data/arabidopsis/xiang/tair10_um Ct_1_R1//tmp/left_kept_reads_seg1.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Ct_1_R1//tmp/left_kept_reads_seg1.fq - > Ct_1_R1//tmp/filedfyEff
bowtie -q --un Ct_1_R1//tmp/left_kept_reads_seg2_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 /data/arabidopsis/xiang/tair10_um Ct_1_R1//tmp/left_kept_reads_seg2.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Ct_1_R1//tmp/left_kept_reads_seg2.fq - > Ct_1_R1//tmp/fileLAZ8vP
bowtie -q --un Ct_1_R1//tmp/left_kept_reads_seg3_missing.fq --max /dev/null -v 2 -p 4 -k 10 -m 10 /data/arabidopsis/xiang/tair10_um Ct_1_R1//tmp/left_kept_reads_seg3.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Ct_1_R1//tmp/left_kept_reads_seg3.fq - > Ct_1_R1//tmp/filetn8y1D
/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 Ct_1_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 Ct_1_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 Ct_1_R1//tmp/left_kept_reads_seg1_missing.fq,Ct_1_R1//tmp/left_kept_reads_seg2_missing.fq,Ct_1_R1//tmp/left_kept_reads_seg3_missing.fq /data/arabidopsis/xiang/tair10_um.fa Ct_1_R1//tmp/segment.juncs Ct_1_R1//tmp/segment.insertions Ct_1_R1//tmp/segment.deletions Ct_1_R1//tmp/left_kept_reads.fq Ct_1_R1//tmp/left_kept_reads.bwtout Ct_1_R1//tmp/left_kept_reads_seg1.bwtout,Ct_1_R1//tmp/left_kept_reads_seg2.bwtout,Ct_1_R1//tmp/left_kept_reads_seg3.bwtout
/Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/juncs_db 3 25 Ct_1_R1//tmp/TAIR10_GFF3_genes_transposons.juncs,Ct_1_R1//tmp/segment.juncs /dev/null /dev/null /data/arabidopsis/xiang/tair10_um.fa
bowtie-build Ct_1_R1//tmp/segment_juncs.fa Ct_1_R1//tmp/segment_juncs
bowtie -q -v 2 -p 4 -k 10 -m 10 Ct_1_R1//tmp/segment_juncs Ct_1_R1//tmp/left_kept_reads_seg1.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Ct_1_R1//tmp/left_kept_reads_seg1.fq - > Ct_1_R1//tmp/file8gx9qs
bowtie -q -v 2 -p 4 -k 10 -m 10 Ct_1_R1//tmp/segment_juncs Ct_1_R1//tmp/left_kept_reads_seg2.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Ct_1_R1//tmp/left_kept_reads_seg2.fq - > Ct_1_R1//tmp/fileSnCay9
bowtie -q -v 2 -p 4 -k 10 -m 10 Ct_1_R1//tmp/segment_juncs Ct_1_R1//tmp/left_kept_reads_seg3.fq | /Net/fs1/home/xianggan/bin/tophat-1.2.0.Linux_x86_64/fix_map_ordering --fastq Ct_1_R1//tmp/left_kept_reads_seg3.fq - > Ct_1_R1//tmp/filepnhEQ2
/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 Ct_1_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 Ct_1_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 Ct_1_R1//tmp/left_kept_reads.fq Ct_1_R1//tmp/TAIR10_GFF3_genes_transposons.juncs,Ct_1_R1//tmp/segment.juncs /dev/null /dev/null Ct_1_R1//tmp/left_kept_reads_seg1.bwtout,Ct_1_R1//tmp/left_kept_reads_seg2.bwtout,Ct_1_R1//tmp/left_kept_reads_seg3.bwtout Ct_1_R1//tmp/left_kept_reads_seg1_to_spliced.bwtout,Ct_1_R1//tmp/left_kept_reads_seg2_to_spliced.bwtout,Ct_1_R1//tmp/left_kept_reads_seg3_to_spliced.bwtout > Ct_1_R1//tmp/left_kept_reads.fq.candidate_hits.sam
sort -k 1,1n --temporary-directory=Ct_1_R1//tmp/ Ct_1_R1//tmp/fileQP7jq7 Ct_1_R1//tmp/left_kept_reads.fq.candidate_hits.sam > Ct_1_R1//tmp/fileBCzf5T
sort -k 1,1n --temporary-directory=Ct_1_R1//tmp/ Ct_1_R1//tmp/fileQP7jq7 Ct_1_R1//tmp/left_kept_reads.fq.candidate_hits.sam
mv Ct_1_R1//tmp/fileBCzf5T Ct_1_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 Ct_1_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 Ct_1_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 Ct_1_R1//junctions.bed Ct_1_R1//insertions.bed Ct_1_R1//deletions.bed Ct_1_R1//tmp/accepted_hits.sam Ct_1_R1//tmp/left_kept_reads.fq.candidate_hits.sam Ct_1_R1//tmp/left_kept_reads.fq
samtools view -S -b Ct_1_R1//tmp/accepted_hits.sam > Ct_1_R1//tmp/fileAGQm4q
samtools sort Ct_1_R1//tmp/fileAGQm4q Ct_1_R1//accepted_hits