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DrosophilaGenomeEvolution / TrEMOLO

Transposable Elements MOvement detection using LOng reads
GNU General Public License v3.0
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Questions about the sample. #22

Open abcyulongwang opened 1 month ago

abcyulongwang commented 1 month ago

Thank you for developing this excellent software！ I have 20-30 genomes and about 100 long read ONT data. However, the long reads and genomes are not sequenced from the same individual, but belong to different varieties of the same species. Is it suitable to use TrEMOLO for group TE detection in this case? In addition, does this software support genotyping of second-generation sequencing data for subsequent results? This will be an important part for me.

Looking forward to your reply Sincerely yulong

M-D75 commented 1 month ago

Hi,

Indeed, the fact that the long reads and assemblies do not come from the same individual is not necessarily a problem. It can slightly affect the detection accuracy depending on several factors, such as a high divergence (excluding TE) between individuals. However, it depends on the cases and can be more complex.

Unfortunately, the tool does not support short reads, but this could be an interesting update to consider. However, I recommend the tool GraffiTE, which might meet your needs in this scenario.

Best regards, M-D

abcyulongwang commented 1 month ago

Thanks for your reply and recommendation, it is very useful to me.

Best regards