This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Deduplication using UMItools

I have some RNAseq data with a high duplication rate but the reads have UMI (Unique Molecular Identifiers). The UMI length is 5 bp. I have used umitools dedup to remove duplications. When I checked the duplication with MarkDuplicates tools (Picard) still the duplication is a bit high for some samples.

I would expect to have a low or even zero % duplication rate after using UMItools. Is there any explanation?

Could the length of UMI be the reason?

Thank you in advance!

rna-seq bam umitools duplication picard
• 3,779 views • link
updated by Devon Ryan Devon Ryan • written by Ati • Ati

1 answer

Picard should be completely ignored if you have UMIs, as it doesn't use UMIs and will therefore give inflated duplication rates (picard reports PCR duplicates determined using the position of read ends, whereas umitools uses that information in addition to UMI sequence). If you have used umitools dedup then the actual duplication rate is 0, regardless of what picard may report.

• 0 views • link
written by Devon Ryan Devon Ryan

@Devon Ryan Thank you! Even if the UMI length is short (5bp)?

• 0 views • link
written by Ati • Ati

Thank you for your help!

• 0 views • link
written by Ati • Ati

Log in to answer this question.

More posts like this