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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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-Nr option #79

Closed EricSHo closed 2 years ago

EricSHo commented 4 years ago

DCC 0.4.8 ubuntu

I have a question about the -Nr option of DCC.

The Westholm data example used -Nr 5 6. The comment said "minimum count in one replicate [1] and number of replicates the candidate has to be detected in [2]" I don't get what do [1] and [2] mean?

Do they mean the following?

  1. At least 5 junction reads per back-splicing site in a sample, and
  2. This back-splicing site must be detected in at least 6 replicates

Thanks, Eric.

tjakobi commented 4 years ago

Hi @EricSHo,

it's kind of both:

-Nr 5,6: at least 5 BSJ counts in at least 6 samples

Does this help?

Cheers, Tobias

EricSHo commented 4 years ago

I need further clarification. How many BSJ in your example, 5 or 5x6=30?

tjakobi commented 4 years ago

Speaking of overall BSJ reads it would be 30, since in each of the 6 samples we require 5 reads (and the samples have independent read sets).