How to create Gene_transcript association matrix with genome version hg19?
1
0
Entering edit mode
8.0 years ago
jack ▴ 950

Hi all,

I need to creat the Gene-transcript association matrix using hg19 reference genome? is there any website which can help me to do it ? I have tried bioMart, but it gives me in the Ensemble format.

So basically I need the gene and transcripts in the following format:

TranscriptID     GeneID
NM_000015    NAT2
NM_000014    A2M
NM_000016    ACADM
Assembly genome alignment R RNA-Seq • 1.6k views
ADD COMMENT
0
Entering edit mode
8.0 years ago
komal.rathi ★ 4.0k

Using Biomart:

Select Dataset -> Skip Filters -> Go to Attributes -> In the Gene section, uncheck Ensembl Gene ID & Ensembl Transcript ID and check Associated Gene Name. Scroll down, in the External References section, check RefSeq mRNA.

ADD COMMENT

Login before adding your answer.

Traffic: 2688 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6