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dieterich-lab / DCC

DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. DCC applies a series of filters and integrates data across replicate sets to arrive at a precise list of circRNA candidates.
https://dieterichlab.org/software/
GNU General Public License v3.0
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`Start-End` not assigned correctly #87

Closed gnilihzeux closed 3 years ago

gnilihzeux commented 3 years ago

Dear author, I found the start-end feature of a circRNA not assigned correctly. Details is as follows:

circRNA chr1_111724942111725414+ DCC intron-exon Should be intron-intron

Actually, this circRNA is very close to a exon with just 2 bp.

My configures is as follows:

GTF: genecode grch37 p13
DCC version: 0.4.7

Thanks.

tjakobi commented 3 years ago

Dear @gnilihzeux,

is it possible, that the annotated gene has multiple isoforms with different exon/intron borders?

DCC tries to merge different transcript per gene for the annotation process, but borderline cases like yours might stem from two transcripts with slightly shifted borders, i.e. the annotation is correct for one transcript but not for the other one.

Cheers, Tobias

gnilihzeux commented 3 years ago

Thanks, @tjakobi . Just like you said.