Sequences with molecular indexes processing

Question

[Manu Prestat]

Hi, I have some sequencing files which include 8nt molecular indexes on both ends. So I remove them before mapping to the genome, and now I would like to deduplicate the reads with same molecular indexes. I found https://github.com/mbusby/AddUMIsToBam but not sure it is maintained and properly tested (and could not compile as, I think, some header files are missing) which theoretically would be good option when followed by a picard deduplicate step.

Would you have any experience or suggestion for this?

Thanks, Manu

Answer 1

[i.sudbery]

Check out our UMI-tools package design to do UMI deduplication while accounting for sequencing errors in the UMI sequences. https://github.com/CGATOxford/UMI-tools

Pre-print available on Biorxiv: http://biorxiv.org/content/early/2016/05/10/051755

Hope this helps. Get in contact if you need anything more.