two different junction type for the same circ?

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/

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two different junction type for the same circ? #37

Open alexey0308 opened 7 years ago

alexey0308 commented 7 years ago

Hi @tjakobi , is it correct to report two different junction types for the same circ coordinates? The linear transcript counts are the same for both of them (see attached). I think, only the first circ must be reported.

./CircCoordinates:3 63912588 63913225 ATXN7 1 + exon-exon
./CircCoordinates:3 63912588 63913225 N/A 2 - exon-exon

Regards, Alex bug.txt

CDieterich commented 7 years ago

Which data set are you using ?

alexey0308 commented 7 years ago

It is from the MCF7 results.

grep 63912588 /prj/MCF7_RNA_turnover_Naarmann/preprocessing/workflow/DCC/CircCoordinates

CDieterich commented 7 years ago

Ok, then it is indeed stranded RNA-seq and a case that we should look at in detail.

tjakobi commented 6 years ago

I'm not sure that this is an DCC issue. Looking in the junctions files provided to DCC I can see that there is something on the '-' strand that barely gets over the threshold. If I remember the format of the junctions files correctly, the splice type reported there is also 2 which is passed through by DCC.