User: josmos43

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josmos430
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Posts by josmos43

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Impact of k-mer length for kraken2 database
... I am analysing 125bp paired-end metagenomic data, using kraken2 for taxonomic classification. I am running into memory issues, since I am using a very large custom Database. The size of the database is significantly decreased without removing sequences, when I increase the k-mer length. Currently i ...
sequence written 12 months ago by josmos430
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unifrac distances for WGS data with qiime2
... I am doing my first downstream analysis on metagenomic WGS data. I was classifying the taxonomy kraken2 (custom database - all refseqs) and calculating species abundances with bracken. My Idea was to use qiime2 to calculate unifrac distances, since it provides nice plotting features. I obtained th ...
software error written 14 months ago by josmos430 • updated 13 months ago by Biostar ♦♦ 20
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Comment: C: NCBI Taxonomy IDs for Kraken-Silva Database
... I solved the issue buy using "ktImportText" instead, creating the text file from the kraken report ...
written 14 months ago by josmos430
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NCBI Taxonomy IDs for Kraken-Silva Database
... I am trying to run Kraken2 on 16S data, using the Kraken2-Silva database (built with "*kraken2-built --special silva*). The taxonomic IDs listed in column 5 of the kraken report does not correspond to the NCBI Taxonomy. (I need the correct IDs to visualize the results with Krona) I am trying to fi ...
rna-seq written 16 months ago by josmos430 • updated 11 months ago by lara.h.urban0

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