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?
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 :-)