This is a test version of Biostars. For the public version, visit https://www.biostars.org.
QC cut off for snRNAseq data

Hi all,

Apologies if this is a silly question as I am very early on in my bioinformatics journey! I have been playing with an snRNAseq dataset in Seurat and I am currently performing QC on the dataset. Alot of the profiles look like those shown below 1.

So my understanding of the QC step is to remove of situations when we have multiple cells in a well/just debris in a well. From the examples I have seen, the "tail" on nFeature_RNA tends to be alot thinner than the data I have, and so I am slightly unsure of the course of action! Would a suitable cutoff here be something like 600< nFeature <3000, percent.mt<5. percent.rib <2. Or am I misunderstanding what those values above nFeature_RNA > 3000 are?

Many thanks in advance for the help!

Example of distribution of the nFeatures in my reads

rnaseq snrnaseq scrnaseq seurat
• 2,376 views • link
updated by rpolicastro rpolicastro • written by AFP3 • AFP3

1 answer

Instead of semi-arbitrarily picking thresholds, I tend to gravitate towards the MAD strategy outlined here. It's more easily reproduced and scales better once you start having more samples.

• 0 views • link
written by rpolicastro rpolicastro

Log in to answer this question.

More posts like this