output length of tandem repeats

[jorondo1]

Hi, I am trying to figure out how to estimate the total length of tandem repeats found in a sequence and I can't figure out which metric to use. I have several genomes I would like to analyse, I would be interested in how to generate this data from TRF output, do you have any recommendation ?

[bricoletc]

(Not a maintainer of this project but) what exactly do you mean by 'total length'? Sum of Pattern size * copy-number for all repeats identified in a sequence? Or all locations in a sequence covered by at least one tandem repeat?

[jorondo1]

I want to find out what % of the genome is tandem repeats. Would Pattern size * copy-number / genome length be the way to go?

[bricoletc]

Not quite- you'd need to account for positionally-overlapping repeats. I guess ideal would be a BED output describing locations of all the tandem repeats, followed by bedtools genomecov for example.

Bed output already requested in #12. I'd actually be happy to propose an implementation, but it seems like maintainers are not responsive overall - @yzhernand @GaryEBenson ?

[tomsauv]

Hi,
This is couple years old now but In case this is still of any help, you may use the following script to get total length of detected tandems.

https://github.com/tomsauv/TROP-Tandem-Repeat-Overlap-Parser

The script merge the coordinates of overlapping tandem to get total length.

Hope this helps