PAC to transcript_name

Question

[int11ap1]

Good morning,

I have a set of PAC names:

Bra010450    Bra010450    22722931
Bra010450    Bra010450    22722932

And I'd like to obtain the transcript name (for instance, Bra010450.1, Bra010450.2, etc.). I use for this BioMart in R using the BioMart of Phytozome. Nevertheless, BioMart gives to me the same transcript name for the two PAC ids shown (Brassica rapa). What can I do?

Thanks.

Answer 1

[Bert Overduin]

When I use the web interface, filter for the PAC Transcript ID and then choose the PAC Transcript ID and the Transcript Name as attributes, I get:

PAC Transcript ID   Transcript Name
22722931  Bra010449
22722932  Bra010450

[int11ap1]

using biomaRt in R, it gives the same transcript_id. Do you know why?

[Bert Overduin]

No, I have no idea. As I assume that the web interface runs from the same database that biomaRt queries, I suspect that the problem must lie in either your query or biomaRt / Bioconductor.

[Bert Overduin]

What does your biomaRt query look like?

[int11ap1]

Never mind... I'll use http://www.phytozome.net/biomart/martview/ . Thanks for all!