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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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Question: mRNA counts in LinearCount file #61

Closed knuppd closed 5 years ago

knuppd commented 5 years ago

Hi Dieterich-lab,

Just a quick question - Are the Chimeric.Junction.out counts in the LinearCount file the raw counts for the host-mRNA at the location of the circExons? I.e. if you have a 2-exon circRNA and the chimeric.junction.out counts are 200,300,250 for your 3 biological replicates, do these counts only reflect the linear reads aligning to the 2 exons of the circRNA?

Thanks!

tjakobi commented 5 years ago

Hi @knuppd,

the linear counts are counted for the region of the circRNA candidate (i.e. the region defined by the back splice junction) and is line-by-line paired between circRNA and linear counts.

Given your example, the LinearCount file would include the read counts for the region of the two exons. In theory this may also contain reads from the circularized exons - but since we cannot distinguish between those and "normal" linear reads, all non-junction reads are counted as linear reads.

Cheers, Tobias