Add optional UMI handling

[ewels]

From @ewels on August 21, 2017 8:46

It would be nice to add optional handling of UMIs, probably using this project: https://github.com/CGATOxford/UMI-tools

Copied from original issue: SciLifeLab#145

[ewels]

From @TomSmithCGAT on August 21, 2017 9:31

Hi @ewels - Let us know how you get on integrating UMI-tools into your pipeline. Very happy to help out via GitHub issues if you have any questions/issues etc

If you haven't already seen it, we have just released a quick scRNA-Seq tutorial: https://github.com/CGATOxford/UMI-tools/blob/master/doc/Single_cell_tutorial.md

[ewels]

Thanks @TomSmithCGAT! Yes I was just reading over it this morning. I particularly like the TL;DR; section at the top 😉

Whilst the single-cell / 10X analysis looks great, we're not currently running single cell projects in our facility so I think that we should probably keep things simple and just run umi_tools extract and umi_tools dedup if the pipeline is run with --bc-pattern. To be honest, my gut feeling is that single-cell data is different enough to warrant a totally separate pipeline anyway.

Phil

[ewels]

ps. How did you find this issue so quickly..??

[ewels]

From @TomSmithCGAT on August 21, 2017 10:8

Oh yeah, I'd assumed you were wanting to support UMIs for bulk RNA-Seq. Agree a separate pipeline is the best approach for scRNA-Seq.

I sporadically check who the new github stars are from (the speed was just by chance!). I saw you were at SciLife so I searched for "UMI-tools" in the organisation's github just to see what you were using UMI-tools for as we don't really have a very good idea what our user base actually is. We only really hear from people who have issues/questions etc - hopefully that's not everyone!

[ewels]

Aha, ok good to know - I was wondering if there was some magic notification service that I wasn't aware of 😉

[ewels]

From @TomSmithCGAT on August 21, 2017 13:17

No, that would be brilliant though!

[drpatelh]

Can we close this issue now @grst due to the work you done in #435?

[grst]

Yes, this is resolved. Too bad auto-close only works on the master branch...