hi all - my lab is running into an issue where one lab member ran the Peppro proseq pipeline and a different lab member ran the nf-core/nascent pipeline and we're running into wildly differing levels of apparent data quality in re: bigwig scanning. We think the issue is that the lab member using nf-core/nascent didn't use the

--with_umi

parameter when there are 6mer dog-tags at the beginning of each read. When I was looking through the parameters of the nf-core scripts, I couldn't tell where/how the umi are extracted prior to performing

umi_tools dedup

or how to specify the dog-tag length (N{6} in our case). Did I miss a parameter or code snippet somewhere or will

--with_umi

should be sufficient to handle?

Hi, @Michael Bale! Slack uses channels to organise discussions. Press the

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more option on the left sidebar. Then hover over Your organisation, and finally select Channels to browse. Each nf-core pipeline has it’s own channel (e.g. #CE8SSJV3N). Please post any questions about specific pipelines in the relevant channel. If you’re not sure where to post your message, please ask @mashehu for help.