Question: Creation Of A .Bed File From .Txt
0
gravatar for tom.d.brocklehurst
4.6 years ago by
United Kingdom
tom.d.brocklehurst0 wrote:

I have downloaded a subset of data I need to keep from a dataset and it has saved the file as ".txt", how do I convert the .txt file to .BED file so I can use the bed file for further QC testing?

text file plink • 2.3k views
ADD COMMENTlink written 4.6 years ago by tom.d.brocklehurst0
2

You'll need to post a portion of the text file to get any help. Even .bed files are text files.

ADD REPLYlink written 4.6 years ago by Devon Ryan84k

Sure. Here's a portion of the text file:

148594_H10_1958_BC1041075    1
148594_H05_1958_BC1041082    1
120437_F01_BLOOD321047    1
120444_E12_BLOOD321899    1
120438_A04_BLOOD321231    1
ADD REPLYlink modified 4.6 years ago by Devon Ryan84k • written 4.6 years ago by tom.d.brocklehurst0
2

I have no idea what those are IDs for and google only finds them in this post. You'll need to mention where you got this or what the nature of these IDs are.

ADD REPLYlink modified 4.6 years ago • written 4.6 years ago by Devon Ryan84k

BED format description here. As a minimum you require chromosome, start and end positions. Do these exist in your file? If not, you cannot convert directly.

ADD REPLYlink modified 4.6 years ago • written 4.6 years ago by Neilfws48k
2

PLINK .bed (for "binary .ped") is not the same thing as UCSC BED (for "Browser Extensible Data") format...

ADD REPLYlink written 4.6 years ago by chrchang5233.9k

Right. Original questioner needs to clarify that (I see plink as a tag, but need more information than that).

ADD REPLYlink written 4.6 years ago by Neilfws48k

My apologies and am using plink so the files I need are .bed. The file I have kept from the binary dataset is a .txt file and I then need to QC on the extracted data. The first QC I need to perform is a MAF (plink --file mydata --maf 0.05) but it states I cannot do this because I do not have a .ped file, so do I need to create a .ped or .bed file for this?

ADD REPLYlink modified 4.6 years ago • written 4.6 years ago by tom.d.brocklehurst0
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