/share/pkg.7/tophat/2.1.1/install/bin/tophat --no-coverage-search -o /scratch/7056804.1.linga/tophat2 -G RefSeq_GeneBody.gtf -p 16 --library-type fr-firststrand -r -86 --mate-std-dev 150 Bowtie2Index/genome SRR6833764_1.fastq.gz SRR6833764_2.fastq.gz
/share/pkg.7/tophat/2.1.1/install/bin/gtf_juncs RefSeq_GeneBody.gtf  > /scratch/7056804.1.linga/tophat2/tmp/RefSeq_GeneBody.juncs
#>prep_reads:
/share/pkg.7/tophat/2.1.1/install/bin/prep_reads --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir /scratch/7056804.1.linga/tophat2/ --max-multihits 20 --max-seg-multihits 40 --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 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --max-insertion-length 3 --max-deletion-length 3 -z gzip -p16 --inner-dist-mean -86 --inner-dist-std-dev 150 --gtf-annotations RefSeq_GeneBody.gtf --gtf-juncs /scratch/7056804.1.linga/tophat2/tmp/RefSeq_GeneBody.juncs --no-closure-search --no-coverage-search --no-microexon-search --library-type fr-firststrand --aux-outfile=/scratch/7056804.1.linga/tophat2/prep_reads.info --index-outfile=/scratch/7056804.1.linga/tophat2/tmp/%side%_kept_reads.bam.index --sam-header=/scratch/7056804.1.linga/tophat2/tmp/genome_genome.bwt.samheader.sam --outfile=/scratch/7056804.1.linga/tophat2/tmp/%side%_kept_reads.bam SRR6833764_1.fastq.gz SRR6833764_2.fastq.gz
#>map_start:
/share/pkg.7/tophat/2.1.1/install/bin/gtf_to_fasta --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir /scratch/7056804.1.linga/tophat2/ --max-multihits 20 --max-seg-multihits 40 --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 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --max-insertion-length 3 --max-deletion-length 3 -z gzip -p16 --inner-dist-mean -86 --inner-dist-std-dev 150 --gtf-annotations RefSeq_GeneBody.gtf --gtf-juncs /scratch/7056804.1.linga/tophat2/tmp/RefSeq_GeneBody.juncs --no-closure-search --no-coverage-search --no-microexon-search --library-type fr-firststrand RefSeq_GeneBody.gtf Bowtie2Index/genome.fa /scratch/7056804.1.linga/tophat2/tmp/RefSeq_GeneBody.fa > /scratch/7056804.1.linga/tophat2/logs/g2f.out
/share/pkg.7/bowtie2/2.3.4.1/install/bin/bowtie2-build /scratch/7056804.1.linga/tophat2/tmp/RefSeq_GeneBody.fa /scratch/7056804.1.linga/tophat2/tmp/RefSeq_GeneBody
/share/pkg.7/tophat/2.1.1/install/bin/bam2fastx --all /scratch/7056804.1.linga/tophat2/tmp/left_kept_reads.bam|/share/pkg.7/bowtie2/2.3.4.1/install/bin/bowtie2 -k 60 -D 15 -R 2 -N 0 -L 20 -i S,1,1.25 --gbar 4 --mp 6,2 --np 1 --rdg 5,3 --rfg 5,3 --score-min C,-14,0 -p 16 --sam-no-hd -x /scratch/7056804.1.linga/tophat2/tmp/RefSeq_GeneBody -|/share/pkg.7/tophat/2.1.1/install/bin/fix_map_ordering --bowtie2-min-score 15 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --sam-header /scratch/7056804.1.linga/tophat2/tmp/RefSeq_GeneBody.bwt.samheader.sam - - /scratch/7056804.1.linga/tophat2/tmp/left_kept_reads.m2g_um.bam | /share/pkg.7/tophat/2.1.1/install/bin/map2gtf --sam-header /scratch/7056804.1.linga/tophat2/tmp/genome_genome.bwt.samheader.sam /scratch/7056804.1.linga/tophat2/tmp/RefSeq_GeneBody.fa.tlst - /scratch/7056804.1.linga/tophat2/tmp/left_kept_reads.m2g.bam > /scratch/7056804.1.linga/tophat2/logs/m2g_left_kept_reads.out
/share/pkg.7/tophat/2.1.1/install/bin/bam2fastx --all /scratch/7056804.1.linga/tophat2/tmp/right_kept_reads.bam|/share/pkg.7/bowtie2/2.3.4.1/install/bin/bowtie2 -k 60 -D 15 -R 2 -N 0 -L 20 -i S,1,1.25 --gbar 4 --mp 6,2 --np 1 --rdg 5,3 --rfg 5,3 --score-min C,-14,0 -p 16 --sam-no-hd -x /scratch/7056804.1.linga/tophat2