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3.9 years ago
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Hi there. I've encounter a problem when using the genomescope2 to distinguish the allotetraploid and the autotetraploid. My analysis pipeline:
- fastp (filtering)
- using kmc to generate the kmer frequency spectrum
- using kmc_tools to get the histogram
- using genomescope2 to get the final results.
When I do the sample one by one, the results show that most of them are allotetraploid, but when I merge the samples to each corresponding clade, then do the analysis, the results show that nearly all of the clades are autotetraploid. Each raw data (paired-end) is about 3.5G, the merged data is about 15G~20G. The estimated genome size is about 300M. So is the problem of sequencing depth? I'll really appreciate it, if somebody could give me some hint.
