MT and rRNA gene expression in bulk RNA-seq sample QC filtering

Question

[noodlejackson]

Hi everyone,

As part of quality control in bulk RNA-seq, are MT and rRNA expression used to filter out poor quality samples?

Thank you!

Answer 1

[jared.andrews07]

Sometimes, people will assess rRNA content as part of standard pipelines (e.g. looking at percentage of reads aligning to various gene biotypes) or if it seems there may be a problem during downstream analyses. However, ribo depletion and polyA selection are very robust, and this should generally not be an issue unless something went quite wrong during sample handling or library prep.

I have not seen MT expression used to filter bulk RNA-seq samples.

[noodlejackson]

Thank you very much