how to to download a BED file from ucsc to directory using linux

Question

[kimkes25]

Hello, my goal : to download a BED file as desribed here to my directory using linux commands . in the meantine, I am trying to download the wanted file directly in the following way:

my try to download a BED compressed file from the ucsc website:

I go into the table browser(tools>Table Browser):

when I try to click " get output " I see this:

and when I click "get BED" another chrome tb is opened with direct table. wht doesnt it save it on the computer in a gzip BED file ?

Answer 1

[GenoMax]

Right click on the BED output you see in the new chrome tab. Choose "Save As" and save the file to your local computer with "file.bed" (or any name of your choice). SCP/SFTP the file over you your machine. Gzip the file using gzip file.bed.

[kimkes25]

it saves is as a text file this way

[GenoMax]

BED format is plain text. Not sure why you wanted it gzipped, but you do then you need to gzip it yourself.

[kimkes25]

before the gzip issue- when I try to save it as ".bed" it saves it as "bed.txt" and I want it as "bed"

[GenoMax]

Choose "all files" under the format drop-down, enclose your file name in quotes "file.bed". That should save it without the .txt extension. You can also do mv file.bed.txt file.bed to rename the file you already have.

Answer 2

[Luis Nassar]

Hello,

In order to prompt a file download (instead of having the results displayed on your browser) you have to type a name into the output filename field. e.g.

We also offer almost our entire data (with a few clinical exceptions) on our download server if you wish to access them via your terminal (https://hgdownload.soe.ucsc.edu/downloads.html).

If you have any follow up questions, our public help desk can always be reached at [e-mail]. You may also send questions to [e-mail] if they contain sensitive data. For any Genome Browser questions on Biostars, the UCSC tag is the best way to ensure visibility by the team.