Bedtools: How to save output in Cygwin by creating a bed file?

Question

[allyson1115ar]

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?

[PoGibas]

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.

Answer 1

[David W]

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 :-)

[allyson1115ar]

Solved. Thanks.