Usage of the smartseq vs. 10x runs commands unclear

[Leonievb]

The run10x positional argument allows running trex on 10x Chromium data which have UMIs. Smartseq2 data don't have UMIs and for this purpose the smartseq3 positional argument was added (the name of the argument is wrong and should be smartseq2). However, smartseq3 produces data with UMIs and there is currently no way to run trex on this. Therefore the following should be done:

• [x] Smartseq3 positional argument renamed to Smartseq2
• [ ] help section/documentation updated on what it means to run trex with Smartseq2 argument (no UMIs)
• [x] #13

[marcelm]

The main branch only has the run10x subcommand. Smart-Seq2 functionality is currently only in the (incorrectly named) smartseq3 branch. Should that branch be merged?

[marcelm]

I’ve taken the liberty of editing your original post so that the items it contains are formatted as a to-do list.

[marcelm]

I have renamed the smartseq3 branch to smartseq2 and also added a commit to the branch that changes the subcommand name to smartseq2.

[marcelm]

I’ve converted the third item to a separate issue.

[Leonievb]

It would make sense to merge the smartseq2 branch into the main branch to make it easily available

[marcelm]

Ok, I’ll send an e-mail to confirm with Michael.

[marcelm]

I have merged the branch now. I would usually open a PR for something like this, but there were some merge conflicts that were a bit tricky to fix, so I just did the merge "by hand".