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.
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.
Thank you very much for your reply; I will try running Velocyto without that option then.
Log in to answer this question.
