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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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Check correctness of stranded work flow #32

Open tjakobi opened 7 years ago

tjakobi commented 7 years ago

Current runs show circular RNA candidates that are located within an annotated gene but on the different strand. Is this biological reality or maybe an error in the stranded workflow?

CDieterich commented 7 years ago

Well, antisense transcription exists, but should be rare.

We can look at it together next week

Am 30.09.2016 um 18:08 schrieb Tobias Jakobi notifications@github.com:

Current runs show circular RNA candidates that are located within an annotated gene but on the different strand. Is this biological reality or maybe an error in the stranded workflow?

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enuka commented 7 years ago

Hi,

We also encountered the same problem. It is strange because a) about half are reported to be "antisense" b) many of the circRNAs that were reported to be "antisense" are actually reported elsewhere as sense circRNAs. Maybe it is a problem with reading the output of STAR? Could you please advise?

Thanks, Joshua

tjakobi commented 7 years ago

Dear Joshua,

I'm aware of the problem and tray to find some time for fixing the issue as soon as possible as it also delaying the next release of DCC. However, it may take a few more days to release a fixed version.

Thank you for your patience, Tobias

CDieterich commented 7 years ago

Hi Tobias,

I have run the polysome sequencing date from the eLife Doudna paper (PMID: 26735365), which is unstranded. Same problem on hg38

2 20254863 20256170 PUM2 1 - exon-exon
2 20278583 20327378 not_annotated 2 + intergenic-intergenic 2 20326261 20327378 PUM2 1 - exon-exon

The second row is yet another circle in PUM2, which happens to be assigned (randomly?) to the wrong strand. I suggest to assign strand by annotation file or by splice signals.