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how does ENCODE call CLIP-seq peaks spanning exon-exon junctions in mature transcripts?

I was trying to make sure I understand how the ENCODE analysis pipeline handles peaks that span exon-exon junctions in mature transcripts since the coordinates are genome based. Does the peak get split? Does the start and stop span the intron in between? Neither of these sound like they make a ton of sense. If someone could provide some insight, or point me towards the proper documentation that can help me understand, that'd be great. Thanks!

encode clip-seq
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updated by Ram Ram • written by krysta.lianne.engel • krysta.lianne.engel

1 answer

The peaks are split, according to this tool/preprint https://github.com/BackofenLab/CLIPcontext https://www.researchsquare.com/article/rs-18225/v1

And another peak caller PureCLIP suggest that if you want CLIP peaks on mature RNAs, consider mapping to mRNA instead of genome https://pureclip.readthedocs.io/en/latest/PureCLIPTutorial/index.html

ENCODE standard pipeline can be found here https://github.com/YeoLab/eclip consider read the .docx in the doc/ folder It's pretty complicated, I have to admit.

The peak caller ENCODE use is here https://github.com/YeoLab/clipper/tree/master/clipper

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written by Charlene Hsuan-lin Her • Charlene Hsuan-lin Her

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