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griffithlab / regtools

Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.
https://regtools.readthedocs.org
MIT License
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cis-splice-effects identify -j option not writing to file #47

Closed yang-yangfeng closed 7 years ago

yang-yangfeng commented 7 years ago

-j option will print to stdout, even if -j option is supplied with file name

yang-yangfeng commented 7 years ago

actually, upon inspecting the log file, it seems like -j option is not even printing bed12 file of aberrant junctions to stdout

yang-yangfeng commented 7 years ago

Here's the command I ran, and the job successfully completed

/gscmnt/gc2502/griffithlab/yafeng/regtools/build/regtools cis-splice-effects identify -j hcc1395/output/normal_cse_identify_junctions.tsv hcc1395/germline.vcf.gz hcc1395/normal_rna_alignments.bam GRCh37.fa /gscmnt/gc2602/griffithlab/regtools/Homo_sapiens.GRCh37.87.gtf

gatoravi commented 7 years ago

Nice catch! Thanks for finding this.