Feature request: Support for 10x "flex" fixed RNA data

COMBINE-lab / alevin-fry

🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.

https://alevin-fry.readthedocs.io

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Feature request: Support for 10x "flex" fixed RNA data #120

Open pakiessling opened 1 year ago

pakiessling commented 1 year ago

Hi,

10x has a newish product "flex" that allows for the sequencing of fixed nuclei.

It works based on a set of 20 000 probes that bind transcripts and are then captured and sequenced.

The only option I see so far for processing the output FASTQ's is cell ranger multi.

It would be great to have support for this in alevin-fry and I think this fixed RNA protocol will become much more wide spread as it is awesome for multiplexing and FFPE samples.

Let me know if you need any other information and thanks for considering :)

ATpoint commented 1 year ago

+1 though a duplicate of https://github.com/COMBINE-lab/alevin-fry/issues/85

Flex is the rebranded name of what formerly was 'Fixed RNAAssay Kit'.

rob-p commented 1 year ago

Hi @ATpoint,

I agree that support for this seems like it will be really useful (and important) at this point. @DongzeHE: Can we investigate the protocol and see what we'd need to do to support it?

--Rob

DongzeHE commented 1 year ago

According to its user guide from 10X, I don't think there is any difference between processing this kind of data with processing 10X Chromium v3.