Question: pre-mRNA GTF reference for 10x
gravatar for V
1 day ago by
V220 wrote:


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

ADD COMMENTlink modified 1 day ago by piyushjo470 • written 1 day ago by V220

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

ADD REPLYlink written 1 day ago by V220

I am not a CellRanger user so I cannot comment on this pipeline. I personally use Alevin for the lowlevel processing. For the sake of completeness, here is the script I use to create a transcriptome that creates both spliced and unspliced transcripts which are ready to be used with the Alevin preprocessing workflow. For CellRanger, someone else needs to give instructions.

ADD REPLYlink modified 1 day ago • written 1 day ago by ATpoint34k
gravatar for piyushjo
1 day ago by
piyushjo470 wrote:

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.

ADD COMMENTlink modified 23 hours ago • written 1 day ago by piyushjo470

Thank you I will try this out :)

ADD REPLYlink written 1 day ago by V220
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