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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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duplicate reads in the count matrix with difference expression value? #104

Open mathavanpu opened 1 year ago

mathavanpu commented 1 year ago

Hi, I have done the circular RNA prediction, the files CircCoordinates,CircRNACount,CircSkipJunctions and LinearCount generated. The CircRNACount file has duplicate rowname with different expression values. Can you please guide me on this Screenshot from 2022-08-05 13-15-27

gnilihzeux commented 1 year ago

Hi, @mathavanpu Has the problem been solved? I‘m very concerned about this as DCC is the main part in my analysis workflow.

CDieterich commented 1 year ago

Hi @gnilihzeux and @mathavanpu

what kind of sequencing library do you use and does the backsplicing junction fall into a known exons ?

gnilihzeux commented 1 year ago

Generally rRNA-deleted library or rRNA-deleted & RNase R. Actually, I doubt these duplicates represent circRNAs in positive and negative strands seperatly.

tjakobi commented 1 year ago

Dear @gnilihzeux,

Thank you for reporting back. I thought this issues was solved, I will check my commits.

Did you observe similar cases in your data analysis? If so, which DCC version are you using?

Thank you,

Tobias