Find Gene name Chromosome Positions

[omerfaruk]

Hello,

I would like to have an tab-delimited txt file that includes chromosome name, nucleotide start-stop, gene name.

That is;
The gene positions on chromosomes. Something like:
chr start stop name
1 69090 70008 OR4F5
1 861321 874870 SAMD11

Best regards,
Omer Faruk

[mattia]

Try with Ensebl tool
-->
Click on "customise your download".
Then select "ENSEMBL GENES 71 " and your species.
Now, appears : "Filter"s and "Attributes". Click in "Attributes" and then in "Genes".
choose: "Chromosome Name","Gene Start", "Gene Stop", "Associated Gene Name".
Click on "RESULT"
select "TSV" and "Unique result only".
Click on GO.

You can visit also UCSC Genome Browser

[Richard Finney]

For human hg19 ...

Download this file : http://hgdownload.cse.ucsc.edu/golde...refFlat.txt.gz

wget is good way to do this :
wget http://hgdownload.cse.ucsc.edu/golde...refFlat.txt.gz

unzip it :
gunzip refFlat.txt.gz


Then run this ...
cut -f1,3,5,6 refFlat.txt | awk '{print $2"\t"$3"\t"$4"\t"$1}'

[crazyhottommy]

if you know how to use galaxy
watch this video http://screencast.g2.bx.psu.edu/flash/TAF1.html

there is a step getting the genes from UCSC table browser.

[ramouna]

The output is based on hapmap positions right?

[vishal.rossi]

you can get this from Conifer tools, it contains a file called probes.txt which has this information

[jaumesastretomas]

Why are duplicated genes in different chromosomes?

Hi all!

I tried using the VIM option to the refFlat.txt file, but I'm getting duplicated gene names in different chromosomes.

For instance, i'm getting gene MIR6859-3 in chromosome 1, 15 and 16, how is that possible?

what is the best way to get a file with: chrm start end gene_name

[mastal]

MIR looks like it's probably an miRNA, so it's very possible.

See miRBase for more information.

http://www.mirbase.org/