Cellranger sequencing

Question

[crx6xw]

Does cellranger scrnaseq normalize counts to transcript length?

Answer 1

[ATpoint]

Not that I am aware of. Unlike methods such as salmon it does genome alignment and does not resolve the exact transcript expression composition. Counts are just gene-level counts without modification (other thsn UMI deduplication).

As 10x Chromium is end-tagged anyway I am not convinced length correction would be robust or meaningful here.