Total number of genes in hg38

Question

[Glory Basumata]

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

[natasha.sernova]

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

[Glory Basumata]

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

[WouterDeCoster]

Hi Glory Basumata,

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

Cheers,
Wouter

[Glory Basumata]

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

[WouterDeCoster]

No problem and welcome to biostars. Interesting guidelines for posting can be found in the following posts:

• How To Ask Good Questions On Technical And Scientific Forums
• How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
• How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking

[ATpoint]

What have you tried?

Answer 1

[Jorge Amigo]

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

[Glory Basumata]

Thank you Jorge. This helped me.

Answer 2

[WouterDeCoster]

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

[Glory Basumata]

Thank you for your help WouterDeCoster.

Answer 3

[GenoMax]

GENCODE has a statistics page for this information.

[Glory Basumata]

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