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Hi fbreitwieser ,The web site https://fbreitwieser.shinyapps.io/pavian/ can not support krakenuniq --report-file .Or i missed something. The formats are as follows.
% reads taxReads kmers dup cov t…
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To interpret the learned codes it would help to have the following visualizations:
1. distance matrix clustering for all TFs. Do probes from like families cluster together?
2. Visualizatio…
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I'm trying to index a small graph, but the `vg index` command just keeps working at 100% cpu forever. Or, at least I assume it's forever, since `construct` generated the graph in a few seconds, but `i…
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Hello
I am running these commands:
`~/kmergwas/bin/list_kmers_found_in_multiple_samples -l kmers_w_strand_path -k 31 --mac 5 -p 0.2 -o kmers_to_use`
`~/kmergwas/bin/build_kmers_table -l kmers_w_s…
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Dear KrakenUniq team,
I have a theoretical question - I was wondering if you could suggest something here. I am using KrakenUniq to classify bacterial reads from RNA-seq experiments. The database …
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Hi,
I need some clarification regarding the unclassified reads, and how to classify reads when my species is not present in the database.
I have sequenced the genome of a green alga (Chlorophyt…
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On top of my head:
- [ ] When loading `seq` via `bio.FASTA`, comparisons often fail because `s'a' != s'A'` (and most FASTAs are soft-masked and thus contain loads of lowercase letters). One has to …
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For example: https://github.com/vgteam/vg#mapping
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If your graph is large, you want to use vg index to store the graph and vg map to align reads. vg map implements a kmer based seed and extend ali…
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Hi
Is mmseqs deterministic? When running linclust on a large FASTA file of proteins, one would expect to get very similar clusters when rerunning the same command on the same fasta file (with defau…