Building genome index for non-10X platform

[andrewjkwok]

Hi,

I'm looking to do some RNA velocity analysis, but with data from the BD Rhapsody. It looks like for me to to use the loompy fromfq command, I'll need to build a genome index - however, in the notebook about this (https://github.com/linnarsson-lab/loompy/blob/master/notebooks/build_index.ipynb), it's explicitly said that the index built following those instructions is only suitable for 10X data.

Looking into the code, I see that this is partly to do with the 10X barcode whitelists. My question is - if I manage to get barcode whitelists of the Rhapsody platform I'm using, can I follow the same instructions in the notebook to build an index and then run the loompy fromfq command, or are there still other issues that make loompy uncompatible with the Rhapsody data that I have?

Many thanks in advance.

[scSeqLiubice]

Hey,
Bumping this old Issue.

I am also interested in this. I could just imagine that we don't see that many discordant polyT sites expressed, since the library preparation differs in regard of the amplification PCR step.

Best,
Fabian