/oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --no-novel-juncs -p 8 --GTF /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation.gtf --transcriptome-index /oak/stanford/groups/akundaje/marinovg/genomes/hg20/transcriptome-indexes/gencode.v25.annotation -o Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized.fa
/oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/gtf_juncs /oak/stanford/groups/akundaje/marinovg/genomes/hg20/transcriptome-indexes/gencode.v25.annotation.gff  > Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/tmp/gencode.juncs
#>prep_reads:
/oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.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 Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/ --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 --bowtie1 -z gzip -p8 --gtf-annotations /oak/stanford/groups/akundaje/marinovg/genomes/hg20/transcriptome-indexes/gencode.v25.annotation.gff --gtf-juncs Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/tmp/gencode.juncs --no-closure-search --no-coverage-search --no-microexon-search --fasta --aux-outfile=Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/prep_reads.info --index-outfile=Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/tmp/left_kept_reads.bam.index --sam-header=Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/tmp/hg38-male_genome.bwt.samheader.sam --outfile=Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/tmp/left_kept_reads.bam Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized.fa
#>map_start:
/oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/bam2fastx --all --fastq Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/tmp/left_kept_reads.bam|/oak/stanford/groups/akundaje/marinovg/programs/bowtie-0.12.9/bowtie -q -v 2 -k 60 -m 60 -S -p 8 --sam-nohead --max /dev/null /oak/stanford/groups/akundaje/marinovg/genomes/hg20/transcriptome-indexes/gencode.v25.annotation -|/oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/fix_map_ordering --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --bowtie1 --sam-header Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/tmp/gencode.v25.annotation.bwt.samheader.sam - - Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/tmp/left_kept_reads.m2g_um.bam | /oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/map2gtf --sam-header Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/tmp/hg38-male_genome.bwt.samheader.sam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/transcriptome-indexes/gencode.v25.annotation.gff - Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/tmp/left_kept_reads.m2g.bam > Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/logs/m2g_left_kept_reads.out
#>tophat_reports:
/oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.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 Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/ --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 --bowtie1 -z gzip -p8 --gtf-annotations /oak/stanford/groups/akundaje/marinovg/genomes/hg20/transcriptome-indexes/gencode.v25.annotation.gff --gtf-juncs Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/tmp/gencode.juncs --no-closure-search --no-coverage-search --no-microexon-search --sam-header Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/tmp/hg38-male_genome.bwt.samheader.sam --report-discordant-pair-alignments --report-mixed-alignments --samtools=/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools --bowtie2-max-penalty 6 --bowtie2-min-penalty 2 --bowtie2-penalty-for-N 1 --bowtie2-read-gap-open 5 --bowtie2-read-gap-cont 3 --bowtie2-ref-gap-open 5 --bowtie2-ref-gap-cont 3 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/hg38-male.fa Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/junctions.bed Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/insertions.bed Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/deletions.bed Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/fusions.out Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/tmp/accepted_hits Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/tmp/left_kept_reads.m2g.bam Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/tmp/left_kept_reads.bam
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/tmp/accepted_hits0.bam Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/tmp/accepted_hits0_sorted
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/tmp/accepted_hits1.bam Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/tmp/accepted_hits1_sorted
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/tmp/accepted_hits2.bam Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/tmp/accepted_hits2_sorted
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/tmp/accepted_hits3.bam Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/tmp/accepted_hits3_sorted
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/tmp/accepted_hits4.bam Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/tmp/accepted_hits4_sorted
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/tmp/accepted_hits5.bam Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/tmp/accepted_hits5_sorted
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/tmp/accepted_hits6.bam Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/tmp/accepted_hits6_sorted
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/tmp/accepted_hits7.bam Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/tmp/accepted_hits7_sorted
/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools merge -f -h Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/tmp/hg38-male_genome.bwt.samheader.sam Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/accepted_hits.bam Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/tmp/accepted_hits0_sorted.bam Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/tmp/accepted_hits1_sorted.bam Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/tmp/accepted_hits2_sorted.bam Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/tmp/accepted_hits3_sorted.bam Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/tmp/accepted_hits4_sorted.bam Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/tmp/accepted_hits5_sorted.bam Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/tmp/accepted_hits6_sorted.bam Cas13-sgRNAs.gencode.v25.sense_intronic.UT.finalized-TopHat-2.0.8-GENCODEv25/tmp/accepted_hits7_sorted.bam
#>alldone: