UCSC knownCanonical hg19 vs. hg38
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7 weeks ago
Sanjar ▴ 90

I searched at UCSC Genome Browser's website, but couldn't find relevant information.

The hg19 version of the canonical transcripts (knownCanonical) has 32K entries whereas hg38 version (GENCODE based) has 66K entries.

What accounts for this 2x difference?

genome UCSC hg19 hg38 canonical • 162 views
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A: which annotation I should for RNA-seq? Ensembl, UCSC or refseq?

You are not only comparing two different genome builds here but also two different consortia (RefSeq vs GENCODE). Ensembl uses GENCODE, see linked answer.

Also: https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-16-S8-S2

Or simply search for Gencode vs RefSeq on the web, there are many posts addressing this.

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Yes, it's RefSeq vs. GENCODE. But still it amazes me that there's 2x difference in canonical transcripts.

A canonical transcript is linked to a gene (maybe not strictly, but if we consider a cluster a gene that's what it translates to). So does that mean that when we use hg19/RefSeq based canonical transcripts, we are missing half of expressed regions?

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