Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: Convert .txt in to .bed format to upload into Galaxy
0
gravatar for c.s.karandeni-dewage
2.8 years ago by
c.s.karandeni-dewage • 0
c.s.karandeni-dewage • 0 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 • 3.2k views
ADD COMMENT • link •
modified 2.8 years ago by matthias.desmet • 150 • written 2.8 years ago by c.s.karandeni-dewage • 0

CKP! i have the same problem. Have you find the solution at that problem? Thank u

ADD REPLY • link written 7 months ago by simomll • 0
1
gravatar for matthias.desmet
2.8 years ago by
matthias.desmet • 150
Belgium
matthias.desmet • 150 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 COMMENT • link written 2.8 years ago by matthias.desmet • 150

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 REPLY • link written 2.8 years ago by c.s.karandeni-dewage • 0
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 175 users visited in the last hour