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PAC to transcript_name

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.

biomart
• 3,730 views • link
updated by Ram Ram • written by int11ap1 int11ap1

1 answer

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
• 2 views • link
updated by Ram Ram • written by Bert Overduin Bert Overduin

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

• 2 views • link
written by int11ap1 int11ap1

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.

• 2 views • link
written by Bert Overduin Bert Overduin

What does your biomaRt query look like?

• 0 views • link
written by Bert Overduin Bert Overduin

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