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piosierra / pantera

Identification of transposable element families from pangenome polymorphisms
MIT License
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which famdb library？ #4

Open 1690078218 opened 1 week ago

1690078218 commented 1 week ago

Hello, I am currently using the test.gfa file you provided to reproduce the results. However, when using the Dfam TE tools, I am unsure which dataset from the famdb library to use for comparison and classification, resulting in many N (unknown bases) in the classification results. Could you please let me know which famdb library you used? I would greatly appreciate your help. Thank you!

piosierra commented 1 week ago

Hello, thanks for trying pantera. You can use the Astatotilapia calliptera library. Bear in mind that this is a toy gfa composed build from just one chromosome, to limit the file size, intended just as a way to check the instalation, and the model results may not match 100% the sequences in the library which have been produced with larger alignments from the whole genome.

1690078218 commented 1 week ago

thanks,I will try it