Entering edit mode
5.1 years ago
MatthewP
★
1.4k
My data is WGS not RNA-seq.
My STAR-Fusion command
./STAR-Fusion --CPU 10 --genome_lib_dir /hg19/GRCh37_gencode_v19_CTAT_lib_Oct012019.plug-n-play/ctat_genome_lib_build_dir --left_fq /rawdata/1.clean.fq.gz --right_fq /rawdata/2.clean.fq.gz --output_dir /output
--genome_lib_dir
file download from https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/
Rsult files
$ls
Aligned.out.bam Log.out ReadsPerGene.out.tab star-fusion.fusion_predictions.abridged.tsv _STARgenome
Chimeric.out.junction Log.progress.out SJ.out.tab star-fusion.fusion_predictions.tsv _STARpass1
Log.final.out pipeliner.6993.cmds _starF_checkpoints star-fusion.preliminary
*predictions.tsv/*predictions.abridged.tsv
is empty, Chimeric.out.junction
seems normal(size 2.2G), I will show 3 lines
1 chr_donorA brkpt_donorA strand_donorA chr_acceptorB brkpt_acceptorB strand_acceptorB junction_type repeat_left_lenA rep
1 eat_right_lenB read_name start_alnA cigar_alnA start_alnB cigar_alnB num_chim_aln max_poss_aln_score non_ch
1 im_aln_score this_chim_aln_score bestall_chim_aln_score PEmerged_bool readgrp
2 chr4 99453489 - chr10 9844169 + -1 0 0 CL100124340L1C001R008_555048 99453490 150M 9844170 150
2 M 3 300 156 294 294 0 GRPundef
3 chr4 128129935 - chr10 9844169 + -1 0 0 CL100124340L1C001R008_555048 128129936 58M18357N92M 984
3 4170 150M 3 300 156 294 294 0 GRPundef
All logs and screen output is normal, no error. Maybe the reason is no result passed filtering
* Running CMD: /App/STAR-Fusion-v1.8.0_FULL/util/filter_likely_RT_artifacts.pl /output/sta
r-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass-filter_likely_RT_artifacts: (pass: 0, filtered: 6)
* Running CMD: /App/STAR-Fusion-v1.8.0_FULL/util/remove_lesser_candidates_at_breakpoint.pl /output/star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass-filter_lesser_candidates_at_breakpoint: (pass: 0, filtered: 0)