Total number of genes in hg38
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3.3 years ago

I am studying RNA-Seq data and I need to know how many genes are incorporated in reference genome h38 build (UCSC) ?

RNA-Seq • 1.8k views
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This was this article in 2015.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4339237/

See Figure 4 there. Three databases had their own opinions.

28442 for UCSC at that time

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Hi Natasha, thank you for sharing the paper. I now have the answer to my question.

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Hi Glory Basumata,

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.
Upvote|Bookmark|Accept

Cheers,
Wouter

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Thanks for the update Wouter. I am a new user here in this community, so I didn't know about upvote :) Cheers!

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What have you tried?

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5
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3.3 years ago

locate refGene file, uncompress it, look for the 13th column containing gene names, make sure there are no repetitions, and count them:

curl http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/refGene.txt.gz \
| zcat | cut -f13 | sort -u | wc -l
28054
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Thank you Jorge. This helped me.

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3.3 years ago

These metrics are summarized by Ensembl (for their annotation) at https://www.ensembl.org/Homo_sapiens/Info/Annotation

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Thank you for your help WouterDeCoster.

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3.3 years ago
GenoMax 108k

GENCODE has a statistics page for this information.

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Hi genomax, thank you for sharing the weblink. I now have rough estimate of the no. of genes to work with.

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