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how to combine two output of RepeatMasker?

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?

repeatmasker repeats next-gen
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written by kk.mahsa kk.mahsa

Please post example input and expected output example

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written by cpad0112 cpad0112

1 answer

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
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written by ATpoint ATpoint

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

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written by kk.mahsa kk.mahsa

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