Hello,

If the reference genome is in UCSC and has a RefSeq track, then you can extract a file with the transcript and protein identifiers from the Table Browser called "refLink" and subset it for rows in your query RefSeq transcript identifiers.


If the RefSeq data is at BioMart or another source, a similar path to the one I outline below will work with some modifications, it all depends on the file format, but Galaxy's tools can manipulate data is just about every way you will need.

Using a transcript identifier query, subset protein identifiers in a UCSC RefSeq track:

A.
Load your list of NM* identifiers ("Get Data -> Upload).
- set the file format to "tabular" (use "pencil" icon to "Edit Attributes -> Change data type") if needed.

B.
Load RefSeq id mapping data with "Get Data -> UCSC Main" and set the form parameters as needed, choosing the track "RefSeq Genes" and the table "refLink". Make sure the region is the entire genome. Send to Galaxy formatted as-is (tabular).

B.
Next, cut columns 3 and 4 out of the table with tool "Text Manipulation ->Cut" and the options "c3,c4".

C. OPTIONAL, if you want the full list of coding RefSeqs for another purpose... remove the non-coding RefSeqs with the tool "Filter and Sort -> Select" and the options "that: NOT Matching" and "the pattern: ^NR_.*$". Be sure to enter the regular expression '^NR_.*$' without any quotes.

D. Perform a join using "Join, Subtract and Group -> Compare two Datasets" with the options>:
    - "Compare: <file of trans and prot id, filtered or not>"
    - "Using column: c1" where c1 is the trans ids
    - "against: <file of trans ids>"
    - "and column: c1" where c1 is the trans ids
    - "To find: Matching rows of first dataset"

E.
Result dataset is a two column tabular file:
   transcript id <tab> protein id


Hopefully this helps you and others who are doing a similar task. If you think you will be doing this a lot, be sure to consider extracting the steps into a workflow.

Thanks for using Galaxy,

Jen
Galaxy team



On 10/27/11 1:34 PM, Li, Jilong (MU-Student) wrote:
Hi,

I have some refseq gene id, like NM_*****.

How can I transfer these gene id into protein id, like NP_****?

Thank you very much!

Victor


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