Question: Start /end of genes in plink (.bim , .bed , .fam) files
0
gravatar for marwa.cs91
3.7 years ago by
marwa.cs9120
Egypt
marwa.cs9120 wrote:

Hello all, I am new in plink analysis, 

How can I search in plink files for location (start / end)of gene for example CD2AP gene in which its location on chromosome 6: base pairs 47,477,745 to 47,627,262

Thanks in advance

.fam plink genes .bed .bim • 1.2k views
ADD COMMENTlink modified 3.7 years ago by Philipp Bayer6.3k • written 3.7 years ago by marwa.cs9120
0
gravatar for Philipp Bayer
3.7 years ago by
Philipp Bayer6.3k
Australia/Perth/UWA
Philipp Bayer6.3k wrote:

I think you're looking for the --make-set command in plink:

http://pngu.mgh.harvard.edu/~purcell/plink/dataman.shtml#makeset

Given a file of genes in this format:

Chromosome start end ID

Plink will give you a file with a set of SNPs located in that range for each gene in your input list

ADD COMMENTlink written 3.7 years ago by Philipp Bayer6.3k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1565 users visited in the last hour