Question: Does RefSeq DB have a CDS file for its transcripts?
0
gravatar for pwg46
6.0 years ago by
pwg46440
United States
pwg46440 wrote:

Hello,

I am looking for a file which contains all CDS for their NM (coding transcript) identifiers. Ensembl has one which maps each of its ENST's to their CDS, however I have been unable to find the same for Refseq's coding transcripts (NM). If anyone knows of and could point me to such a file, that would be great. It doesn't even have to come from RefSeq databases. Perhaps there are other NCBI db's which have the file I'm looking for?

 

cds refseq coding sequence nm • 2.4k views
ADD COMMENTlink modified 6.0 years ago by Irsan7.2k • written 6.0 years ago by pwg46440
1
gravatar for Irsan
6.0 years ago by
Irsan7.2k
Amsterdam
Irsan7.2k wrote:
  1. Go to UCSC table browser
  2. Select genes and gene prediction tracks
  3. Select RefSeq genes
  4. select table refGene
  5. region: genome
  6. output format: bed
  7. refGene-CDS.bed
  8. Click on get output
  9. select coding exons
ADD COMMENTlink modified 6.0 years ago • written 6.0 years ago by Irsan7.2k

Hmm, I looked into that. However the data file it outputs doesn't give the actual sequences. Are there any adjustments I could make to get the actual sequence?

ADD REPLYlink written 6.0 years ago by pwg46440
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