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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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The meaning of warning message #97

Closed m-kouhsar closed 2 years ago

m-kouhsar commented 2 years ago

Hi I ran the DCC for some paired-end data based on the user guide. It works properly and is completed successfully, but in the log file there are many warning messages like this:

WARNING: circRNA end position ('chr3', '113162019') does not have mapped read counts, treated as 0

What does mean this warning message? Does this message mean DCC sets the count to zero for those circRNAs which they don't have any linear read mapped to the genome? another question is: Do DCC detect novel circRNAs? I need to predict all circRNAs in my data (both novel and annotated). Are there any options that should be set to do this?

Best Morteza

tjakobi commented 2 years ago

Hi @m-kouhsar,

Your assumption is correct in that the message means that no linear reads have been mapped to the circRNA position. However, the "treating as 0" refers to the LinearCount file, not the CircRNACount file.

To answer your second question, yes, DCC predicts novel circRNAs automatically, the annotation is purely used for the assignment to gene names.

Cheers,

Tobias

m-kouhsar commented 2 years ago

Thanks, Tobias