Question: From gene symbol (gene name), TSS id and locus coordinates .. How to get the Refseq RNA (RNA accession number .. NM *******)?!!
0
gravatar for faniastrokes
3.2 years ago by
faniastrokes0 wrote:

Dear All, I got RNAseq data already processed. I have txt file containing "Official gene symbol", "TSS id" and "locus coordinates" and relative "FPKM" value. I need to have the "gene id" (that's fine) and also the Refseq RNA id (NM ....), because I NEED TO KNOW WHICH ISOFORM has this FPKM value. PLEASE help me to understand how can I get this information from gene symbol, TSS id and locus!!

rna-seq • 2.6k views
ADD COMMENTlink modified 3.2 years ago by steve2.4k • written 3.2 years ago by faniastrokes0
1

Always useful to post an example snippet and specify what genome this data is from.

ADD REPLYlink written 3.2 years ago by genomax76k

I apologise! Human Genome, in particular MCF-7 cell lines.

ADD REPLYlink written 3.2 years ago by faniastrokes0
1

You may want to speak with the people who processed the data. It is possible that they generated this at the gene level, rather than the transcript level.

ADD REPLYlink written 3.2 years ago by pld4.8k

I'm pretty sure not all isoforms can be uniquely identified by the information you describe you have.

ADD REPLYlink modified 3.2 years ago • written 3.2 years ago by WouterDeCoster42k

I think one of these might have it?
http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/kgXref.txt.gz

http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz

ADD REPLYlink written 3.2 years ago by steve2.4k

This one http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz has Chromosome, strand (+ or -), gene_id, gene_symbol and RNA accession number. But I couldn't understand the other columns .. I need the locus coordinates; to link them to the different RNA accession number.

ADD REPLYlink written 3.2 years ago by faniastrokes0
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