Question: Total number of genes in hg38
0
gravatar for Glory Basumata
4 months ago by
India/Guwahati/Indian Institute of Technology Guwahati
Glory Basumata10 wrote:

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

rna-seq • 342 views
ADD COMMENTlink modified 4 months ago by WouterDeCoster34k • written 4 months ago by Glory Basumata10
2

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

ADD REPLYlink modified 4 months ago • written 4 months ago by natasha.sernova3.1k

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

ADD REPLYlink written 4 months ago by Glory Basumata10
1

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

ADD REPLYlink written 4 months ago by WouterDeCoster34k

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

ADD REPLYlink written 4 months ago by Glory Basumata10

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

ADD REPLYlink written 4 months ago by WouterDeCoster34k

What have you tried?

ADD REPLYlink written 4 months ago by ATpoint9.3k
5
gravatar for Jorge Amigo
4 months ago by
Jorge Amigo11k
Santiago de Compostela, Spain
Jorge Amigo11k wrote:

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
ADD COMMENTlink modified 4 months ago • written 4 months ago by Jorge Amigo11k

Thank you Jorge. This helped me.

ADD REPLYlink written 4 months ago by Glory Basumata10
4
gravatar for WouterDeCoster
4 months ago by
Belgium
WouterDeCoster34k wrote:

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

ADD COMMENTlink written 4 months ago by WouterDeCoster34k

Thank you for your help WouterDeCoster.

ADD REPLYlink written 4 months ago by Glory Basumata10
4
gravatar for genomax
4 months ago by
genomax58k
United States
genomax58k wrote:

GENCODE has a statistics page for this information.

ADD COMMENTlink written 4 months ago by genomax58k

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

ADD REPLYlink written 4 months ago by Glory Basumata10
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