gravatar for igor

2 hours ago by

United States

It seems that the definition of "ribosomal genes" in the context of RNA-seq or scRNA-seq QC can be very different. I've seen some people define them by simply grepping for ^Rp[sl] (for mouse), which are technically ribosomal proteins. GENCODE GTF has a rRNA (as well as rRNA_pseudogene and Mt_rRNA) biotype, which marks ribosomal transcripts (includes genes such as Rn5s and n-R5s*).

For the purpose of QC, is one definition (or a combination of the two) more correct? For example, the default 10x Genomics workflow doesn't include rRNA biotypes in the reference, so perhaps that's why people resort to ribosomal proteins in that case.

link

modified 1 hour ago

by

ATpoint46k

written
2 hours ago
by

igor12k



Source link