Bedtools intersect with header file

Question

[irfanwustl]

I have two bedgraph files(a_h.bedgraph and b_h.bedgraph) with header. And I am running the following command:

bedtools intersect -header -wa -a a_h.bedgraph -b b_h.bedgraph

However I am getting the following error:

Error: unable to open file or unable to determine types for file a_h.bedgraph Please ensure that your file is TAB delimited (e.g., cat -t FILE). - Also ensure that your file has integer chromosome coordinates in the expected columns (e.g., cols 2 and 3 for BED).

When I remove the header from a_h.bedgraph and b_h.bedgraph, it works. Is there any way to keep the header after the intersection?

[ATpoint]

I am reasonably sure headers have to be indicated by #, is that the case with your file?

[User000]

I have the same problem, have you resolved?

[ATpoint]

Do you have headers? Did you make sure everything is tab-separated?

[irfanwustl]

Sorry for my late response. Actually, I could not resolve it. Is it a bug?

[ATpoint]

People, User000 and irfanwustl, simply saying "it does not work" is not an adequate error description. As asked twice now above, did you make sure your file is properly tab-separated and headers are indicated by a '#'? I am 99.99% sure this is not a bug and a problem with your files.

[irfanwustl]

Got it. Yes, the header was not indicated by '#'

[User000]

I actually solved the problem 4 months ago I guess, so I do not remember now what was the problem, but it was pretty easy at the end :) and I never said it does not work

Answer 1

[Alex Reynolds]

If you use bash, one option is to use tools that support Unix streams:

$ bedops --intersect <(sort-bed A.txt) <(sort-bed B.txt) | cat <(head -1 A.txt) - > answer.bed

Replace head -1 with adjustments from -1 to whatever number of header lines you have in A.txt.