Question: Bedtools: How to save output in Cygwin by creating a bed file?
0
gravatar for allyson1115ar
3.8 years ago by
allyson1115ar20 wrote:

I am using bedtools intersect to obtain my two bed files overlapped coordinates but my output is too large in cygwin I couldn't copy paste my result. Is there any other ways to save my output in a text file or bed file? 

bed alignment sequence bedtools • 1.8k views
ADD COMMENTlink modified 3.8 years ago by David W4.7k • written 3.8 years ago by allyson1115ar20

Don't want to be sceptical about this Cygwin, but under "normal" linux there shouldn't be any problems. Try ubuntu.

 

:-)

Edit:

I don't know how cygwin works, but bedtools should save it's results into a file. 

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by PoGibas4.7k
1
gravatar for David W
3.8 years ago by
David W4.7k
New Zealand
David W4.7k wrote:

bedtools intersect -a a.bed -b b.bed > intersect_ab.bed

The '>’ bit redirects the output into a (newly created/overwritten) file instead of printing to screen. Welcome to unix-like commands, once you 'get' this and piping you'll find you can do a lot from the command line :-)

ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by David W4.7k

Solved. Thanks.

ADD REPLYlink written 3.8 years ago by allyson1115ar20
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