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ylab-hi / ScanExitron

A computational workflow for exitron splicing identification
MIT License
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Problem working with unstranded data #5

Closed markddesimone closed 1 week ago

markddesimone commented 3 years ago

Hi, I am trying to use ScanExitron but my data is unstranded. regtools therefore writes ? in the strand column and junction_overlap_CDS_to_position_BED prevents any junctions being detected. due to the test: 

if stats == 'N' and strand != '?
e.g. the janno file contains: chrom start end name score strand splice_site acceptors_skipped exons_skipped donors_skipped anchor known_donor known_acceptor known_junction gene_names gene_ids transcripts
chr1 133276 659397 JUNC00000001 1 ? CG-GT 0 0 0 N 0 0 0 NA NA NA

Is there any way to use or modify ScanExitron to work with unstranded data?

thank you

dolittle007 commented 1 week ago

ScanExitron now supports the parameter for RNA-Seq strandness. 0 = unstranded, 1 = first-strand/RF, 2, = second-strand/FR.