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TGAC / KAT

The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra.
http://www.earlham.ac.uk/kat-tools
GNU General Public License v3.0
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specifying the correct homozygous peak #147

Open jflot opened 4 years ago

jflot commented 4 years ago

Hello, I am working with highly heterozygous species (with 2-3% heterozygosity) so it happens to me quite often that kat comp mistakenly chooses the heterozygous peak as the homozygous peak (because the heterozygous peak is the highest peak in my histogram). As a result, the calculations of the genome statistics (genome size, heterozygous rate and assembly completeness) are affected. Is there a way to tell kat comp the index of the actual homozygous peak so that the genome statistics are estimated correctly?

IoanaBrannstrom commented 2 years ago

Hi. Did you get any answers? I am also very interested to find the answer.

bjclavijo commented 2 years ago

I'm afraid there is no way to set the peak manually can you share the .mx files and what your expected output would be vs. what you're getting?