Did you remove PCR duplicates when processing single-cell riboseq data?

mvanins / scRiboSeq_manuscript

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Did you remove PCR duplicates when processing single-cell riboseq data? #1

Closed suluying closed 4 months ago

suluying commented 4 months ago

Hello, Thanks for developing this really interesting methodology. I have a question that did you remove PCR duplicates when processing single-cell riboseq data?

mvanins commented 4 months ago

Hi,

Yes, a 10-nt UMI is attached during the 5' adapter ligation. After alignment, reads are de-duplicated using UMI-tools; the specific settings are here https://github.com/mvanins/scRiboSeq_manuscript/blob/fc5579b299b1d0d5a5408d188d81532c3db2396a/data_processing/templates/deduplicate/deduplicate_position.sh#L1-L8