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Total number of genes in hg38

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

rna-seq
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updated by WouterDeCoster WouterDeCoster • written by Glory Basumata Glory Basumata

What have you tried?

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written by ATpoint ATpoint

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

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written by Glory Basumata Glory Basumata

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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written by WouterDeCoster WouterDeCoster

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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written by Glory Basumata Glory Basumata

3 answers

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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written by Jorge Amigo Jorge Amigo

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

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written by WouterDeCoster WouterDeCoster

Thank you for your help WouterDeCoster.

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written by Glory Basumata Glory Basumata

GENCODE has a statistics page for this information.

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written by GenoMax GenoMax

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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written by Glory Basumata Glory Basumata

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