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GWW / scsnv

scSNV Mapping tool for 10X Single Cell Data
MIT License
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question about -V3_5P #18

Closed ttt-404 closed 1 year ago

ttt-404 commented 1 year ago

Hi,

So sorry to bother you, it’s me again. I’m recently dealing with a scRNA-seq dataset (GSE118056), and the chemical library is 5' VDJ. I noticed that in scSNV, the parameter -l include four options (-V2 -V3 -V2_5P -V3_5P). But I checked the Cell Ranger website (https://kb.10xgenomics.com/hc/en-us/articles/115004506263) and found there’s no 5’ V3, only 5’ V1 and 5’ V2, and they shared the same barcode list (737k-august-2016.txt). So I wonder if the option -V3_5P in -l is incorrect?

Thanks!

GWW commented 1 year ago

Hi,

Thanks for bringing this up.

I included a -V3_5P option mostly for future proofing. The library type is used to control how long the expected UMI and barcode should be:

V3 16 bp barcode, 12 bp UMI V2 16 bp barcode, 10 bp UMI

The 5P and 3P options only change which transcript strand the alignment should be expected on.

ttt-404 commented 1 year ago

Thanks for your patient reply! Now I understand it.

GWW commented 1 year ago

No problem at all!