How to calculate TE density from RepeatMasker result?

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2.3 years ago

haruki ▴ 20

Hello, all

Is there any good way to calculate TE density separated by window size from RepeatMasker result, which I can use circos plot?

Can I count the number of masked bases per window from masked FASTA? ( I don't think this is a good way, because it includes not only TEs, but also Simple Repeats, etc.) Or should I just count the TE length per window from RepeatMasker result such as .out file?

repeatmasker circos elements transposable • 995 views

ADD COMMENT • link 2.3 years ago by haruki ▴ 20

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I think it is better to use the GFF file that repeatmasker outputs. It is easier to parse than the other output formats. The only difficulty will be its potentially large size. If loading the file works out, for example in R, then you could simply run coverage on a GenomicRanges object created from it. Or use BEDtools or similar software to calculate the coverage on a BED-file made from the GFF (with gff2bed).

ADD REPLY • link 2.3 years ago by Michael 54k

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Thank you for your reply!

In my GFF, there are some repeats that are not annotated as TEs, such as Simple_Repeat or Low_complexity. Should I remove these repeats if I want to calculate "TE density"(not repeat density) correctly ? In my results, the percentage of these repeats is less than 1%, so maybe I don't need to worry about them...

ADD REPLY • link 2.3 years ago by haruki ▴ 20

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