Question: Identification of Genes spanning a QTL
2
gravatar for pixie@bioinfo
5.6 years ago by
pixie@bioinfo1.4k
Université Paris, Saclay
pixie@bioinfo1.4k wrote:

Hi E   veryone,

I have a list of QTLs. The chromosome number, start and stop regions are given. I have a list of genes which I want to map onto the regions. I have obtained the locations of the genes from BioMart. I wanted to find out the genes lying in the QTL regions. Is it just a trivial mapping using a script or do I need to consider some other conditions to identify the genes in the QTL region ? Any suggestion will be greatly appreciated.

qtl • 1.5k views
ADD COMMENTlink modified 5.6 years ago by mark.ziemann1.3k • written 5.6 years ago by pixie@bioinfo1.4k

Bedtools is a great option as suggested by Mark. If you have no programming background, you can use UCSC Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables). You can select your organism of interest, select Gene and gene predictions and define multiple locations or list of your QTL locations by clicking on define regions. You can then download data in GTF or bed format.  

ADD REPLYlink modified 5.6 years ago • written 5.6 years ago by Ashutosh Pandey12k
0
gravatar for mark.ziemann
5.6 years ago by
mark.ziemann1.3k
Australia/Mebourne/Geelong/Deakin
mark.ziemann1.3k wrote:

If the QTL coli and gene loci are both in bed format (and the genome build is the same), then you can use bedtools intersect to determine the genes that lie in those regions. 

bedtools intersect -wa -a  genes.bed -b QTLs.bed

Bedtools can also be accessed via Galaxy if you are on a windows machine.

ADD COMMENTlink written 5.6 years ago by mark.ziemann1.3k
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