[Aksiniya Peycheva]

Dear team,

I have a txt file with gene names and since they are about 40000 I am trying to find a way to run the whole list and get their loci information, without having to to it for each gene. Is that possible? It’s for an art project. I would appreciate the help.


Thank you 🙏

[Gerardo Perez]

Hello,

Thank you for your interest in the UCSC Genome Browser and for sending your inquiry.

You can get the loci information using the Table Browser. Your list of gene names would have to match the gene names in a gene track. Here are two gene tracks that we offer for human hg38/hg19 and mouse mm10/mm39:

NCBI RefSeq: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&c=chrX&g=refSeqComposite
GENCODE: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&c=chrX&g=knownGene

You can do the following to get the loci information using a list of gene names and the Table Browser:

1. Navigate to the Table Browser: http://genome.ucsc.edu/cgi-bin/hgTables
2. Select an assembly:

clade: Mammal
genome: Human
assembly: Dec. 2013 (GRCh38/hg38)

3 Select a gene track:

group: Genes and Gene Predictions
track: GENCODE V43
table: knownGene

4. Set the region to “genome”
5. Click paste list or upload list next to “identifiers (names/accessions):” and enter your list of gene names. Then click submit
6. Insert a name next to “output filename”,
7. Set the output format to “Selected fields from primary and related tables”. This will allow you to select fields of interest. Click get output .
8. Select “name”, “chrom”, “txStart”, and “txEnd” fields. These fields will give you the gene name and the coordinates in the genome for the genes.
9. Click get output. The output will then give you the gene name and the gene coordinates for hg38

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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