Genes near SNP within certain window frame and distance
0
0
Entering edit mode
15 months ago

Hi everyone, I have SNPs and genes in bed format in two files, I can see the genes that map to SNP within certain windoframe lets say 200Kb using the following command:

 windowBed -a SNPs.bed -b Gene.bed -w 200000 > snps.withGenesWithin.bed

This command identifies the set of genes within certain windowframe but doesn't provide a distance, whereas the following command provides the genes distance from SNP but wasn't able to find option to cannot specify the window frame.

closest-features --delim '\t' --dist SNPs.bed Genes.bed > answers.bed

Is there any command which I can use to specify the window frame as well as it estimates the genes distance from SNP.

bedops bedtools • 569 views
ADD COMMENT
0
Entering edit mode

Not sure if I am following the question, or what are you looking after, but maybe you could just combine both commands? Something like:

windowBed -a Gene.bed -b SNPs.bed -w 200000 -u > Genes_nearby_SNPs.bed

And then:

closest-features --delim '\t' --dist SNPs.bed Genes_nearby_SNPs.bed > answers.bed

ADD REPLY

Login before adding your answer.

Traffic: 2925 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6