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How can i handle the multimapped reads?

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.

assembly sequencing alignment
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updated by Charlene Hsuan-lin Her • Charlene Hsuan-lin Her • written by PK • PK

1 answer

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

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

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