/usr/local2/tophat-1.4.1.Linux_x86_64/tophat --library-type fr-unstranded --min-anchor-length 8 --splice-mismatches 0 --min-intron-length 70 --max-intron-length 50000 --min-isoform-fraction 0.15 --max-multihits 20 --min-segment-intron 50 --max-segment-intron 500000 --segment-mismatches 2 --segment-length 20 --num-threads 4 assembly-unitigs filtered_106A_Female_Mix_GATCAG_L007_R1.fastq.gz
/usr/local2/tophat-1.4.1.Linux_x86_64/prep_reads --min-anchor 8 --splice-mismatches 0 --min-report-intron 70 --max-report-intron 50000 --min-isoform-fraction 0.15 --output-dir ./tophat_out/ --max-multihits 20 --segment-length 20 --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 50000 --max-mismatches 2 --sam-header ./tophat_out/tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 -z gzip -p4 --no-closure-search --no-microexon-search --library-type fr-unstranded --fastq --aux-outfile=./tophat_out/left_kept_reads.info filtered_106A_Female_Mix_GATCAG_L007_R1.fastq.gz | gzip -c - >./tophat_out/tmp/left_kept_reads.fq.z
gzip -cd< ./tophat_out/tmp/left_kept_reads.fq.z|/usr/local2/bowtie-0.12.7/bowtie -q --un ./tophat_out/tmp/left_kept_reads_unmapped.fq -v 2 -p 4 -k 20 -m 20 --max /dev/null assembly-unitigs -|/usr/local2/tophat-1.4.1.Linux_x86_64/fix_map_ordering -|gzip -c > ./tophat_out/tmp/left_kept_reads.bwtout.z
/usr/local2/tophat-1.4.1.Linux_x86_64/long_spanning_reads --min-anchor 8 --splice-mismatches 0 --min-report-intron 70 --max-report-intron 50000 --min-isoform-fraction 0.15 --output-dir ./tophat_out/ --max-multihits 20 --segment-length 20 --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 50000 --max-mismatches 2 --sam-header ./tophat_out/tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 -z gzip -p4 --no-closure-search --no-microexon-search --library-type fr-unstranded assembly-unitigs.fa ./tophat_out/tmp/left_kept_reads.fq.z /dev/null /dev/null /dev/null ./tophat_out/tmp/left_kept_reads.bwtout.z > ./tophat_out/tmp/left_kept_reads.unspl.bam
/usr/local2/tophat-1.4.1.Linux_x86_64/segment_juncs --min-anchor 8 --splice-mismatches 0 --min-report-intron 70 --max-report-intron 50000 --min-isoform-fraction 0.15 --output-dir ./tophat_out/ --max-multihits 20 --segment-length 20 --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 50000 --max-mismatches 2 --sam-header ./tophat_out/tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 -z gzip -p4 --no-closure-search --no-microexon-search --library-type fr-unstranded --ium-reads ./tophat_out/tmp/left_kept_reads_unmapped.fq assembly-unitigs.fa ./tophat_out/tmp/segment.juncs ./tophat_out/tmp/segment.insertions ./tophat_out/tmp/segment.deletions ./tophat_out/tmp/left_kept_reads.fq.z ./tophat_out/tmp/left_kept_reads.bwtout.z ./tophat_out/tmp/left_kept_reads.bwtout.z
/usr/local2/tophat-1.4.1.Linux_x86_64/juncs_db 3 20 ./tophat_out/tmp/segment.juncs /dev/null /dev/null assembly-unitigs.fa
/usr/local2/bowtie-0.12.7/bowtie-build ./tophat_out/tmp/segment_juncs.fa ./tophat_out/tmp/segment_juncs
/usr/local2/bowtie-0.12.7/bowtie -q -v 2 -p 4 -k 40 -m 40 --max /dev/null ./tophat_out/tmp/segment_juncs ./tophat_out/tmp/left_kept_reads_unmapped.fq|/usr/local2/tophat-1.4.1.Linux_x86_64/fix_map_ordering -|gzip -c > ./tophat_out/tmp/left_kept_reads_unmapped.to_spliced.bwtout.z
/usr/local2/tophat-1.4.1.Linux_x86_64/long_spanning_reads --min-anchor 8 --splice-mismatches 0 --min-report-intron 70 --max-report-intron 50000 --min-isoform-fraction 0.15 --output-dir ./tophat_out/ --max-multihits 20 --segment-length 20 --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 50000 --max-mismatches 2 --sam-header ./tophat_out/tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 -z gzip -p4 --no-closure-search --no-microexon-search --library-type fr-unstranded assembly-unitigs.fa ./tophat_out/tmp/left_kept_reads.fq.z ./tophat_out/tmp/segment.juncs /dev/null /dev/null ./tophat_out/tmp/left_kept_reads.bwtout.z ./tophat_out/tmp/left_kept_reads_unmapped.to_spliced.bwtout.z > ./tophat_out/tmp/left_kept_reads.candidates.bam
/usr/local2/tophat-1.4.1.Linux_x86_64/tophat_reports --min-anchor 8 --splice-mismatches 0 --min-report-intron 70 --max-report-intron 50000 --min-isoform-fraction 0.15 --output-dir ./tophat_out/ --max-multihits 20 --segment-length 20 --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 50000 --max-mismatches 2 --sam-header ./tophat_out/tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 -z gzip -p4 --no-closure-search --no-microexon-search --library-type fr-unstranded --samtools=/usr/local2/samtools-0.1.18/samtools ./tophat_out/junctions.bed ./tophat_out/insertions.bed ./tophat_out/deletions.bed - ./tophat_out/tmp/left_kept_reads.candidates_and_unspl.bam ./tophat_out/tmp/left_kept_reads.fq.z | /usr/local2/samtools-0.1.18/samtools sort - ./tophat_out/accepted_hits