Entering edit mode
2.4 years ago
mahir.firefox
▴
10
Hello everyone,
I'm newbie with plink, I need to do this analysis but I cannot figure out how to convert to ped
and map
files. I have this big document that I was able to transpose in a way that I need, but because it's a big file it takes a lot of time and I could use a help.
I use Linux. I researched that I can do it with PLINK
I have only this file (csv) in my folder.
[firefoxer@firefoxer-pc snip]$ ls plink.log transposed_file_10.csv
I tried like this...
[firefoxer@firefoxer-pc snip]$ plink --ped transposed_file_10.csv --allow-extra-chr
PLINK v1.90b6.26 64-bit (2 Apr 2022) www.cog-genomics.org/plink/1.9/
(C) 2005-2022 Shaun Purcell, Christopher Chang GNU General Public License v3
Logging to plink.log.
Options in effect:
--allow-extra-chr
--ped transposed_file_10.csv
7641 MB RAM detected; reserving 3820 MB for main workspace.
Error: Failed to open .
[firefoxer@firefoxer-pc snip]$ plink --ped transposed_file.csv --map transposed_file.csv --allow-extra-chr
PLINK v1.90b6.26 64-bit (2 Apr 2022) www.cog-genomics.org/plink/1.9/
(C) 2005-2022 Shaun Purcell, Christopher Chang GNU General Public License v3
Logging to plink.log.
Options in effect:
--allow-extra-chr
--map transposed_file.csv
--ped transposed_file.csv
7641 MB RAM detected; reserving 3820 MB for main workspace.
Error: Failed to open transposed_file.csv.
[firefoxer@firefoxer-pc snip]$
How can I convert to ped and map files?
Why are you using ped and map files? There's some valid reasons, but they are very old and inefficient and a different data format is usually better.
I'm student researcher, I'm working on a scientific paper, and this is my first time in this field.
I have SNP data for different apple varieties and I have to do PCA (Principal Component Analysis) and few more analysis (depending of other factors). My research said that I need map and ped files in order to run PLINK for analysis. If this type of files are outdated, what do you recommend to use?
OK.
csv
isn't really a data format, all it says that columns are separated by commas. Please can you post a small sample in your question (edit your original question) so we can see what it looks like and how you could convert it. Thanks.The community standard is VCF. PLINK itself has had better support for VCF than map/ped files for close to a decade.