How can i handle the multimapped reads?

Question

[PK]

Hi all,

I got the CLIP-Seq data to analysis but the main problems is i have more than 60% of reads were multi-mapped. So if i remove the multi-mapped reads i think i may loose some significant candidates (that's just my instinct). What is the best way to handle these multi-mapped reads. should i align with non-coding RNAs. Because the knock-down might have influenced the ncRNA bio-genesis. I got confused at this point. can you please help me..

Thanks in advance.

Answer 1

[Charlene Hsuan-lin Her]

https://github.com/YeoLab/repetitive-element-mapping

the eCLIP pipeline has repetitve element mapping, check the github repo and the paper:

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-01982-9