Selecting appropriate expressed repeat annotation for Velocyto

Question

[merdanosman]

Hi everyone, I have a mouse scRNA-Seq dataset (BDRhapsody) on which I want to run velocyto. On the velocyto CLI usage page, it says I need to "download an appropriate expressed repeat annotation (for example, from UCSC genome browser)". I pre-processed the raw sequencing data by GENCODE release M35 (GRCm39) (release date: 05.2024). When I check the UCSC genome browser for repeats, I see that the newest assembly is Jun 2020 - GRCm39/mm39. Can I use those repeat annotations from UCSC, or should I run repeatmasker on the reference from GENCODE? Even though the GRC versions match, I could not be sure.

Thanks for your help.

Answer 1

[ATpoint]

To be honest, we never do this and simply skip this option. Main reason is that (to my knowledge) there is no proper explanation beyond a one-liner in the original paper (https://www.nature.com/articles/s41586-018-0414-6) that really motivates the use of this option. STARsolo to my knowledge, which can also output spliced counts similar to velocyto, does not do this, and I am not awware alternative pipelines such as alevin-fry or kallisto-bustools pay attention to this in particular.

[merdanosman]

Thank you very much for your reply; I will try running Velocyto without that option then.