Check correctness of stranded work flow

[tjakobi]

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]

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]

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]

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]

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.