how to combine two output of RepeatMasker?

Question

[kk.mahsa]

hi

i run homology-based and denovo identification of repeats using Repeatmasker and Repeatmodeler. Now i have two output that i want to combine them to obtain final content of different repetitive elements. how can i do it? anyone can to help me?

[cpad0112]

Please post example input and expected output example

[kk.mahsa]

example file is here example

Answer 1

[ATpoint]

You mean getting a kind of consensus list from the two files? If so, merge the files using cat and then use BEDtools merge to get consensus intervals:

cat *.bed | sort -k1,1 -k2,2n | BEDtools merge -i - > consensus.bed

[kk.mahsa]

i have two output files (.out) that some elements between them are shared and some are unique. i want to get one file that give me consensus repetitive elements