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shendurelab / LACHESIS

The LACHESIS software, as described in Nature Biotechnology (http://dx.doi.org/10.1038/nbt.2727)
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Determining the value of CLUSTER_N #14

Closed yfu closed 8 years ago

yfu commented 8 years ago

For a genome with an unknown number of chromosomes (we have not karyotyped it yet), it there a good way to determine the number of chromosomes using Hi-C data? I tried to do some simple hierarchical clustering using the data points in heatmap.txt, but I cannot find obvious turning points... Does LACHESIS produce some results that can help one determine the number of chromosomes? Thanks!

JingaJenga commented 8 years ago

The short answer is - No, you can't reliably infer chromosome number. You can get a rough estimate but not a precise one. For more details, see Supplementary Fig. 13 in the Nature Biotech paper (and the paragraph in the Discussion that refers to it.)