Peak caller options in the CLIP-Seq pipeline

Pipelines CLIP
1

The CLIP-seq pipeline uses Clippy peaks for PEKA. Is it possible to include other peak callers, Paraclu or PureClip, as options in the clip-seq pipeline?

*One can see that paraclu is run as part of clip-seq, but its outputs are not used for PEKA. Thus, an alternative option would be to run a ‘PEKA module’ on Flow, where one could choose the individual paraclu-generated peaks (and corresponding crosslink files) as inputs. Is this currently doable?

Thank you.
p

2

Hi Paulo

This is not currently possible on Flow but will be possible in the updated CLIP pipeline we are working on which should be available within the next month. We can also provide PEKA as an individual module like you suggest - will add it to the to-do list!

All best
Charlotte

3

These implementations will be useful. Thank you, Charlotte.

Kind regards,
Paulo