How to create Gene_transcript association matrix with genome version hg19?

Question

[jack]

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

Answer 1

[komal.rathi]

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.