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DerrickWood / kraken2

The second version of the Kraken taxonomic sequence classification system
MIT License
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All my reads are unclassified #748

Open thek71 opened 1 year ago

thek71 commented 1 year ago

Hi, I have the following problem and I am really open to suggestions, as I don't know if my reasoning is wrong or something else. I have genomic reads (ONT and PacBio) from an aquatic plant. We know that because of the conditions the samples we took have bacterial reads in. I used Kraken2 with the nr database to classify the reads, but all my reads are unclassified. I even used a 0 confidence, but the results remained the same. Are there any suggestions on what parameters to use? Should I change the database? I would at least expect to have reads in the eukaryotes taxa.

zhongshuai666 commented 1 year ago

i have some guess, may not be true.

  1. perhas your database dont have matched data
  2. when you build your database, kraken2 need calculate k-mer in enough depth, if you dont use enough depth, --max-db-size in a small number, the outcome may like this, cause i am in same now bracken-build -d $DBNAME -t 12 --max-db-size n
jenniferlu717 commented 9 months ago

What are you command lines for building the nr database/classifying your sampleset?