Closed dn-ra closed 2 years ago
Hi Dan,
It will have limited impact for downstream tasks. But if you want, you can use umi_tools dedup directly, rather than starting from the beginning of umi_tools pipeline.
Cheers, Jon
Thanks Jon, That's really handy advice. Many thanks.
Hi Jon,
I have a query about step c) of the protocol (using umi_tools to collapse PCR duplicates) Is this necessary if I am using the bamfile that has come off cell ranger? I am facing some strange behavior with umi_tools so I'm wondering if this is necessary. I have a 10x 5' GEX library of some 500 million reads.
For background, the issues I'm having are that: 1)
umi_tools extract
is not removing the content of of R1 when it apends the UMI onto the read name of R2. 2) If I grep for a particular barcode+UMI combination in the amended R2 file, I find that the transcripts corresponding to it are not very similar and it makes me wonder if an error has happened somewhere.I appreciate that these points are better to ask to the umi_tools authors, just thought I'd give you some context.
Thanks, Dan