Extract k‐mers specific to germ‐line restricted chromosomes - KamilSJaron/k-mer-approaches-for-biodiversity-genomics GitHub Wiki

2. Extracting k-mers matching certain criteria

Now, that we know how to make the 2d k-mer plot, let's find chromosome-specific k-mers. As no one has actually seen the tse-tse data, we can't write here what threshold we should use, that's something we will need to discuss together dependent on the results of the previous section.

determining thresholds

To show you how the thresholds can be terminted, here we show an example of Bradysia tilicola from Hodson et al. 2021. In this preprint, germ-line restricted chromosomes were isolated by comparing a library made of testes and heads of flies. The karyotypes in the two types of tissues, as well as 2d k-mer spectra, are in the figure 1 from the manuscript

Hence for the isolation of 27-mers corresponding to X, GRC or autosomes respectively we chose the following thresholds (boxed on the image)

A
 - 125 < head   < 175
 - 80  < testes < 140
X
 - 50  < head   < 100
 - 60  < testes < 100
GRC
 - head < 5
 - 15 < testes # this might be too stringent