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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.

Home Page:https://dieterichlab.org/software/

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Grouping of samples and replicates

EricSHo opened this issue · comments

commented

Hi,

My installation is DCC 0.4.8 ubuntu

I have a question about the grouping of samples of replicates.

My data consists of 4 experimental conditions, and 3 replicates per condition.

Should I specify all 4x3=12 Chimeric.out.junction entries in one samplesheet/mate1/mate2? In this case, I run DCC only once.

Or, should I create 4 separate samplesheets/mate1s/mate2s, one for each condition, and each contains 3 replicates? In this case, I need to run DCC 4 times.

Thanks, Eric.

commented

Hi @EricSHo,

generally you can run everything together and later on pull only those circRNAs that are specific for one condition. When you want to use circtest in the next step having a combined table will also make that step easier.

Cheers,
Tobias