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7.1 years ago
ebb11238
•
0
I'm unfamiliar with how to annotate a bedpe
file with the GENOCDE gtf file:
https://www.gencodegenes.org/releases/25.html
My understanding is to use bedtools intersect
, but I'm getting errors:
http://bedtools.readthedocs.io/en/latest/content/tools/intersect.html
Here is the format of my (unsorted) bedpe, file1.bedpe
:
chrom1 start1 end1 chrom2 start2 end2 info
0 1 6469 68470 1 8609 8610 abc3
1 1 8426 8627 5 1076796 1076797 abc3
2 1 14632 14933 1 142491 142492 abc3
3 16 16570 166971 1 167720 167721 abc3
4 1 104384 104985 1 10461 10472 abc3
There are a few more categorial columns (i.e. strand, and other information)
When I try
bedtoools intersect -a file1.bedpe -b gencode.v25.annotation.gtf
I get the error
ERROR: file `file1.bedpe`: has non positional records, which are only valid for the groupBy tool.
What is the correct way to do this?