The total genes items (e.g. ENTREZ ID, SYMBOL) in OrgDb (Salmo salar; [["AH66207"]]) is just half the gene number in NCBI ?!

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wecai • 0

@wecai-20542

Last seen 5.0 years ago

Hi, I try to use the OrgDb object for annotation. I found my mapped items was weight less than the expected. For the quality check, I used keys(AH[["AH66207"]], keytype = "SYMBOL") to check all the enrolled SYMBOL gene term, which turned to be about 57k (NCBI has 97k entries). Could anybody help with that please?

Any suggestions are appreciated.

Colin

Annotationhub Annotationdb profiler annotationdbi • 1.0k views

ADD COMMENT • link 5.0 years ago wecai • 0

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I am not an expert on salmon, but a quick view on NCBI website shows that the number of annotated genes (that all have a gene symbol) indeed equals 57k (to be specific: 57,946 [incl. 6 discontinued genes]). This number is in line with what you reported... In other words, why do you expect 97k gene entries??

Taxonomy browser (see table at right) here. Direct link to all salmon genes here.

ADD REPLY • link 5.0 years ago Guido Hooiveld ★ 3.9k

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