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jenniferlu717 / Bracken

Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
http://ccb.jhu.edu/software/bracken/index.shtml
GNU General Public License v3.0
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For a subset of taxa, bracken is subtracting all kraken2 reads to give 0 #173

Closed phlatphish closed 2 years ago

phlatphish commented 2 years ago

Hi,

I created a partially custom kraken2 database by taking a set of bacterial genomes that were not in the kraken2 database, editing their fasta headers and the seqid2taxid.map, than adding them to the bacterial genomes .fna file. The kraken2 build and the running of kraken2 went perfectly. However, when running bracken on the kraken2 report, all of the reads for my custom set get adjusted to 0.

All of my added genomes are in the taxononomy that is in the kraken2 database folder.

I'm happy to share files with you if that will help.

Thanks

phlatphish commented 2 years ago

Downloading and rebuilding everything made this issues go away.