Failed to open .map

[Katie O'Connor]

Hi everyone,

I am trying to perform a basic association test between 2322 SNPs and a single quantitative phenotype. I have had some tutorials with given files for Plink, but otherwise I am a beginner. 

Whenever I try anything with --file or --bfile I get: "Error: Failed to open Test.map"

I constructed my .ped file in Excel (csv) with columns (as per tutorials):

Family ID

Individual ID

Paternal ID (all 0s)

Maternal ID (all 0s)

Sex (all 0s - I am working with plants that can be both Male and Female)

Phenotype

Then 2 columns with A/T/0 missing for each of 2322 SNPs. (I am also confused about this format as some tutorials talk about bytes, and having to code the SNPs as 00, 01, 11 and 10 ?? and others A/T etc)

I also constructed my .map file in Excel (csv). I am working on a novel species where we only have the marker name and not any location information. Columns:

Chromosome (1s for everything - is this correct?)

Marker ID (snp1-snp2322)

Position in morgans (0 - unknown)

Base pair coordinate (1-2322 - is this correct?)

From what I can tell, I have my two files set up correctly, and that these files should be able to produce bed, bim and fam files.

However, even a seemingly simple command like "plink --make-bed --file Test --out Test.bed" gives the Error Failed to open Test.map.

Any help would be greatly appreciated! Thank you in advance!

[Christopher Chang]

This error means that plink can't find "Test.map".  Where is that file located?

[Katie O'Connor]

Hi, thanks for your reply.

It is in the same directory as the plink program and Test.ped, and this is the folder I am working in.

[Katie O'Connor]

I think I have sorted this out...

I found that you have to copy your data from excel and paste into notepad. This seems to have fixed my .ped and .map files.