I am using the following command
bedtools intersect -wb -a file1.bed -b file2.gff3 > output.txt
In the output I have more entries that are not even present in the file1.bed!
I have tried with sorting and also changing the extension of the file2gff3 to bed but again the same output..
What is the problem?
Is there another tool i can use to do the same? or awk ?