FeatureCounts with scRNA-seq

Question

[fuhaolll2]

Hi,i have seen someone in article quantitate 10X scRNA-seq data with FeatureCount. Can FeatureCount differ the cell barcode? What parameter should i set when quantitate 10X scRNA-seq data with FeatureCount that i can get the cell-gene matrix

[khorms]

Can you add a link to this article?

Answer 1

[ATpoint]

No, featureCounts is not intended for single-cell data. You need specialized software to solve UMIs, extract barcodes etc... CellRanger is the traditional solution, STARsolo is an extension of the STAR aligner, doing pretty much the same thing but much faster, and then there are the leightweight / pseudo/ selective aligners and their single-cell addons such as Alevin (the Salmon extension), BUStools (the kallisto extension) and probably others as well. Strongly suggest to use any of those rather than coming up with custom solutions for a non-trivial problem.

Edit: featureCounts alone (without additional software and depending hpw the BAM file was made) is not suited for single-cell data. You can probably make it work, e.g. as here https://scrnaseq-course.cog.sanger.ac.uk/website/construction-of-expression-matrix.html but again, why bothering when you can use established end-to-end pipelines as the ones mentioned above. If you still want to use it the linked tutorial might be a starter but it sounds like a bother to me.