Which are the different kinds of GeneID that exist?

Question

[pinheirofabiano]

I have raw counts from a RNA-Seq experiment, but the GeneIDs are listed as numbers, they don't look like ensembl or NCBI gene IDs. Here is a picture. Can you help me out?

Answer 1

[GenoMax]

Likely those are NCBI/Entrez ID's (which are numerical). You can look them up using EntrezDirect:

$ esearch -db gene -query 645520 | esummary | xtract -pattern DocumentSummary -element Id,Name 
645520  FAM138A

$ esearch -db gene -query 79501 | esummary | xtract -pattern DocumentSummary -element Id,Name,ScientificName
79501   OR4F5   Homo sapiens

$ esearch -db gene -query 100287102 | esummary | xtract -pattern DocumentSummary -element Id,Name,ScientificName
100287102   DDX11L1 Homo sapiens

Does this match the dataset you are working with?

[pinheirofabiano]

thank you very much, GenoMax I believe you're right, I'm working with human samples.. I need to convert them to gene symbols..

[GenoMax]

You can lookup many ID's by putting them in a file (one per line) and using epost method like so.

$ more names.txt
645520
79501
100287102

$ epost -db gene -input names.txt -format acc | esummary | xtract -pattern DocumentSummary -element Id,Name,ScientificName

79501   OR4F5   Homo sapiens
645520  FAM138A Homo sapiens
100287102   DDX11L1 Homo sapiens