Hi all,
We’ve released a new version of CLIP-Seq pipeline v1.3 - this is a minor update from v1.2, but a useful one!
- Crosslink position can now be chosen as ‘start’, ‘middle’ or ‘end’ - the default is ‘start’ which is the same as its always been. This enables analysis from different protocol types. Note that ‘start’ is read start minus one, and ‘end’ is read end plus one.
- Making crosslinks is now one process called CALC_GENOME(/TRANSCRIPTOME)_CROSSLINKS this should make it easier to find crosslink files.
- Previously, skipping PCR deduplication meant that some later processes wouldn’t run - now all downstream processes run as normal.
- Curated data - now raw crosslink bedgraphs are in the curated data as these are more widely used than the normalised ones.
As always don’t hesitate to get in touch with questions.
Best,
Charlotte