Hello Victor,
RefSeq sequences designated by a transcript identifier formatted as NR_*
are non-coding (meaning: transcribed, but not translated), therefore
there is no protein product and no linked protein sequence NP_* identifier.
This documentation from NCBI covers RefSeq naming conventions:
http://www.ncbi.nlm.nih.gov/RefSeq/key.html
Hopefully this is helpful,
Best,
Jen
Galaxy team
On 10/28/11 3:24 PM, Li, Jilong (MU-Student) wrote:
Hi,
I have some refseq gene id, like NM_***** and NR_******.
I know how to transfer NM_****** into protein ID NP_*****. But, how to transfer
NR_***** into protein id, like NP_****? I do not know. Could you please tell me?
Thank you very much!
Victor
________________________________________
From: Jennifer Jackson [j...@bx.psu.edu]
Sent: Thursday, October 27, 2011 11:23 PM
To: Li, Jilong (MU-Student)
Cc: galaxy-u...@bx.psu.edu
Subject: Re: [galaxy-user] how to transfer gene id into protein id
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
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
