pre-mRNA GTF reference for 10x

Question

[V]

Hello,

Would anyone in the community have a pre-mRNA reference GTF they would be willing to share? (mm10 and GRCh38) Or could point me towards the direction of finding one if they are aware if someone has made theirs available online?

I'd like to be able to map my data to be able to detect introns/exons (spliced/unspliced) transcripts to use with RNA velocity.

Ideally the CellRanger pipeline. These were already aligned by our genomics facility with the standard GTF provided by 10x that does not capture that info, so would ideally need to re-count using a GTF that holds that information. Platform = 10x genomics chromium 3' v3.

Thanks you

[V]

Thanks for modifying initial post to show more detail @ATpoint. Would you happen to have a solution to this or could offer some clarification? :(

Answer 1

[piyushjo]

Cellranger has tutorial how to make Cellranger compliant gtf from your choice of .gtf. They also mention how to convert it into premRNA gtf.

I would like to tell you that in pre-mRNA gtf, genes that are overlapped by other genes will not be counted. For that, you should align the reads to exonic gtf, and replace their counts in intronic alignment.

Also you could use STARsolo, there you can get both alignment in one run and also get output that you can use for RNA velocity.

[V]

Thank you I will try this out :)