Where is the "Refseq genes" from the "track"drop-down menu?

[Lei, Haiyan (NIH/NCI) [C]]

Dear UCSC staff:

                I tried to get the hg30_refseq.bed file. From online search, it should be the following steps, but from the track drop-down menu, I just see the NCBI RefSeq and not the Refseq Genes. I need the same hg38 format with the attached hg19 file. Can you please tell me how I get the same hg38 refseq bed format with the attached hg19 format? Thanks.

Best

Haiyan

[Gerardo Perez]

Hello, Haiyan.

Thank you for your interest in the UCSC Genome Browser and your question about getting hg38 refseq genes in bed format.

Here are two refseq genes tracks that we offer for human hg38:

• RefSeq All (ncbiRefSeq) – all curated and predicted annotations provided by RefSeq.
• UCSC RefSeq (refGene) – annotations generated from UCSC's realignment of RNAs with NM and NR accessions to the human genome. This track was previously known as the "RefSeq Genes" track.

The following FAQ entry can explain the differences between the NCBI RefSeq and UCSC RefSeq tracks:
https://genome.ucsc.edu/FAQ/FAQgenes.html#ncbiRefseq

You can download these data from our download page:
http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/ncbiRefSeq.txt.gz
http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/refGene.txt.gz

You can extract the refseq genes in BED format using the Table Browser. For example, to query the UCSC RefSeq (refGene) on hg38, navigate to the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables) and make the following selections:
1.

clade: Mammal
genome: Human
assembly: Dec. 2013 (GRCh38/hg38)
group: Genes and Gene Predictions
track: NCBI RefSeq
table: UCSC RefSeq (refGene)

2. Set the region to “genome”.
3. Set the output format to “BED - browser extensible data”.
4. Insert a name next to “output filename:”, such as hg38_refGene.bed.
5. Click get output.
6. Then on the “Output refGene as BED” page, click get Bed. The output will then give you a file of all the UCSC RefSeq (refGene) genes for hg38 in bed format.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute

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[Lei, Haiyan (NIH/NCI) [C]]

Hi, Perez:

 

Thanks for the reply. I got the correct format. Have a good weekend!

 

Best

 

Haiyan