Question: PAC to transcript_name
0
gravatar for int11ap1
6.4 years ago by
int11ap1420
Barcelona
int11ap1420 wrote:

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 • 1.6k views
ADD COMMENTlink modified 2.6 years ago by Biostar ♦♦ 20 • written 6.4 years ago by int11ap1420
0
gravatar for Bert Overduin
6.4 years ago by
Bert Overduin3.7k
Edinburgh Genomics, The University of Edinburgh
Bert Overduin3.7k wrote:

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
ADD COMMENTlink modified 9 months ago by RamRS30k • written 6.4 years ago by Bert Overduin3.7k

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

ADD REPLYlink written 6.4 years ago by int11ap1420

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.

ADD REPLYlink written 6.4 years ago by Bert Overduin3.7k

What does your biomaRt query look like?

ADD REPLYlink written 6.4 years ago by Bert Overduin3.7k

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

ADD REPLYlink modified 9 months ago by RamRS30k • written 6.4 years ago by int11ap1420
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