Nguyen Thanh Nguyen comments

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                                            Nguyen Thanh Nguyen

[E::bwa_idx_load_from_disk] fail to locate the index files when running

@xhy1219 hi, you can use the chr6.fa file, just need to change the path inside the get-reads-alt-unmap.sh from chr6.fna to chr6.fa

HLA Truth set

Alright, I see, thank you very much, I will try to see the HLA region from the calls

sampleQC issue

@theodorc Hi, thank you for your answer. My samples are validated by Sanger, some of them contain multiple-exon deletion, when I check the RPKM matrix, I saw that they are...

Systematically determine `min_dist` and `n_neighbors`

yes, I'm actually doing the Hyperparameter Optimization with ARI metric for the particular problem. But I would like to know if there is a more general approach, such as in...

Systematically determine `min_dist` and `n_neighbors`

yes, I was thinking the same. As far as I know, HDBSCAN/DBSCAN employ the `n_sample` parameter, I just don't know how closely related theirs are to UMAP `n_sample` @lmcinnes could...