Question: Convert .txt in to .bed format to upload into Galaxy
0
gravatar for c.s.karandeni-dewage
23 months ago by
c.s.karandeni-dewage0 wrote:

I am trying to get flanking sequence of a list of SNPs. I have the list of SNPs in a excel which I need to convert to the bed format. I looked up for some solution on-line but was not successful. I appreciate any advice on this issue. Thank you.   

galaxy • 1.3k views
ADD COMMENTlink modified 23 months ago by matthias.desmet140 • written 23 months ago by c.s.karandeni-dewage0
1
gravatar for matthias.desmet
23 months ago by
Belgium
matthias.desmet140 wrote:

Hi,


I'm not aware of any tools that can format an excel file to bed. You'll have to manually format the columns following the BED specification (look here: https://genome.ucsc.edu/FAQ/FAQformat.html#format1), export your file to a tab delimited format and manually add the .bed extension.

M

ADD COMMENTlink written 23 months ago by matthias.desmet140

Dear Matthias,

Thanks much for the answer. I did try this before and when I uploaded the file onto Galaxy, it appeared as '.bed.txt'. So, I thought that it would not work. Anyway, it worked at the end. Thanks again. 

CKD

ADD REPLYlink written 23 months ago by c.s.karandeni-dewage0
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