Hi,
I can successfully perform bedtools intersect for two 3-column BED files, but I want to perform the same intersect using a "file A" that contains multiple additional columns with values for a large number of samples formatted like so:
File A:
(chr) (start) (stop) (sample 1..2..3...4...etc..)
chr1 1001 1002 10 25 14 25
chr1 1006 1007 12 22 11 50
chr1 1012 1013 44 11 12 30
File B:
chr1 500 1010
chr1 2000 3000
Output:
chr1 1001 1002 10 25 14 25
chr1 1006 1007 12 22 11 50
Does anyone know if there is a way to use bedtools intersect, or bedtools intersect with another program, or any other code at all into perform this kind of intersect and retain the data in the additional columns in the output?
Thanks!
Dan
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dansapozhnikov •
Not sure if/how your files are sorted, but this should take care of that:
$ bedops -e 1 <(sort-bed fileA.bed) <(sort-bed fileB.bed) > answer.bed
This does not work for me for some reason. It says "Non-numeric end coordinate. See line 1 in fileB.bed". This is not even the problematic file and it worked in bedtools intersect.
If you run cat -te on a few lines of your files, what does it say? For instance what comes out of: head -5 foo.bed | cat -te? Something's up with your files, which needs fixing.
chr1^I2572970^I2579715^M$
See that ^M at the end? That's a Windows carriage return character. You need to remove that. You can use tr for this:
$ tr -d '\r' < foo.bed > foo.fixed.bed
Repeat for all afflicted files, then run your commands on the fixed files.
OK so this seems to be a Windows line ending, so I ran dos2unix. Then I ran bedops as before, and now (unlike bedtools intersect) it ran, but it does not retain the extra columns.
What is the output of this:
$ head -5 fileA.fixed.bed | cat -te
What is the output of this:
$ head -5 fileB.fixed.bed | cat -te
Please post everything you see. The bedops -e command just reports back any elements as they are found, and does not modify them. So either your files are not structured as described, or there is some other problem. If we can see your actual inputs, we can probably figure out what's up.
Thanks to your suggestions I found the problem! File A was space-delimited, not tab. It now runs and retains all the columns. Thank you very much for your help.
Awesome! Glad to help.
Assuming N files A.bed5 through N.bed5 have score data in the fifth column for every position in reference.bed3:
$ bedmap --echo --echo-map-score --delim '\t' --multidelim '\t' reference.bed3 <(bedops -u A.bed5 ... N.bed5) > answer.bed
I think there is a misunderstanding here. There are only two files. One BED (file B) and one BEDGRAPH with 27 columns - chr, start, end, and then one column per sample.
Yes, sorry, I have added it to the original question.
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Have a look at
bedtools unionbedg.Actually, the File A is an output of unionbedg. So it is a bedgraph with many columns and then I want to intersect it with a BED file with intervals. (Also File A has data for each single nucleotide whereas the BED file has intervals)
I added an example to the original post.