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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
BSD 3-Clause "New" or "Revised" License
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zero-length barcode #132

Open wangjiawen2013 opened 5 months ago

wangjiawen2013 commented 5 months ago

Hi, Here is an extreme case where a RNAseq library was constructed without barcodes. That is, there are only umi and biological read in read2 (it also means the length of barcode is zero), Can alevin_fry or simpleaf be used to quantify the gene expression of this library ? Or Let me put this another way, can alevin_fry or simpleaf be used to quantify the gene expression neglecting the barcodes ?

rob-p commented 5 months ago

Hi @wangjiawen2013,

I'm pinging @DongzeHE here for his input. My sense is that it might not be trivial to do this "out of the box", but it's not something that's fundamentally difficult for alevin-fry or simpleaf in any way. In fact, it might even work if you did something silly like, added the same "fake" barcode to every read (e.g. "AAA" or some such).

However, I'm also curious what the use case for something like this might be. In this case, you're basically saying there's one "cell", and so you're just dealing with what sounds like UMI-enhanced bulk RNA-seq. Is there a protocol like this that's in use, or a reason one might want a particular set up like this? As I said, I don't think it's technically challenging, and so if it's useful it's something we could support in a reasonably straightforward manner without e.g. any hacks.

--Rob

wangjiawen2013 commented 5 months ago

We have developed an sequencing technique where a lot of UMI-enhanced bulk RNA-seq are parallel performed. The paper are under preparation now. We think that maybe we can use simpleaf to analyze the data.