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fanglab / nanodisco

nanodisco: a toolbox for discovering and exploiting multiple types of DNA methylation from individual bacteria and microbiomes using nanopore sequencing.
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Binning error - Perplexity is too large #61

Open liorzalayet opened 1 year ago

liorzalayet commented 1 year ago

Hi, I managed to go through all the tutorial with the provided commands and data. Now I'm trying to run the binning function on the Ecoli data that appeared in the earlier steps of the tutorial, however I ran across the following error: 

Error in Rtsne.default(tsne_matrix, check_duplicates = FALSE, perplexity = tsne_perplexity,  :
  Perplexity is too large.
Calls: tsne.motifs.score -> as.data.frame -> Rtsne -> Rtsne.default
Execution halted.

The call is as follows:

image

I tried changing the --tsne_perplexity parameter to lower values (20, 15, 5, 2, 1) with no success. It still prints the same issue and seems to call Rtsne.default(). My nanodisco version is v1.0.3 (latest).

thanks in advance

touala commented 1 year ago

Hello @liorzalayet,

Thank you for trying nanodisco. The issue arise from the type of sample you're trying to analyze. nanodisco binning was designed to processed microbiome datasets with sometimes thousands of contigs. The procedure we implemented is simply not applicable to single bacteria dataset. If you want to try binning, please consult the dedicated tutorial here.

Please let me know if you have any other questions.

Alan