Question: How To Convert Refseq Id To Gene Symbol As Pitx1
4
gravatar for Hamilton
8.3 years ago by
Hamilton280
Hamilton280 wrote:

Hi, how can i convert refseqids (mouse) to gene symbols?

next-gen rna sequencing • 4.0k views
ADD COMMENTlink modified 3.6 years ago by Newgene350 • written 8.3 years ago by Hamilton280
5
gravatar for Pierre Lindenbaum
8.3 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum126k wrote:

you could use the UCSC database for mus musculus:

$ mysql   --user=genome --host=genome-mysql.cse.ucsc.edu -A   -D mm9  \
  -e "select distinct refseq,geneSymbol from kgXref where refseq in ('NM_008866','NM_011541','NM_011011') "
+-----------+------------+
| refseq    | geneSymbol |
+-----------+------------+
| NM_008866 | Lypla1     |
| NM_011011 | Oprk1      |
| NM_011541 | Tcea1      |
+-----------+------------+
ADD COMMENTlink written 8.3 years ago by Pierre Lindenbaum126k
3
gravatar for Newgene
3.6 years ago by
Newgene350
United States
Newgene350 wrote:

use MyGene.info API, python and R clients are available.

For Python:

pip install mygene

then

import mygene
mg = mygene.MyGeneInfo()
mg.querymany(['NM_008866','NM_011541','NM_011011'], scopes='refseq')

that's it!

ADD COMMENTlink written 3.6 years ago by Newgene350
0
gravatar for Curiosity
8.3 years ago by
Curiosity120
Curiosity120 wrote:

You could download refseq gene list in "all" format instead of "BED" format using Galaxy http://main.g2.bx.psu.edu/ and then print the selected columns using unix command.

Use the following command

 awk '{print $2"\t"$13}' all_refseq.list

Ex: NM_001195025 Nuak2

ADD COMMENTlink modified 8.3 years ago • written 8.3 years ago by Curiosity120
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