DECIPHER Package on dada2 -Implementing Silva_metaxa2 training set from qza file into a fastq.gz/.Rdata
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anrongloh • 0
@e1481cea
Last seen 14 days ago
Singapore

Hi there,

Greetings from Singapore! I am currently working on a coral microbiome study on investigating ASVs at different sites and timepoint.

First of all thank you for designing such an excellent package that can be used with the dada2 pipeline to annotate taxonomies on DECIPHER which proved very helpful, especially for someone new to using R for microbiome analysis.

Recently, there was a published study on improving the annotation of unknown ASVs with an expanded Silva_metaxa2 database that has more mitochondrial DNA sequences inside of it to replace the current Silva_r138 training set.

However, the authors made this silva_metaxa2_reference_taxonomy as a qiime2 artifact (qza). The paper can be found here https://www.biorxiv.org/content/10.1101/2021.02.23.431501v1

With their github codes and files stored at https://zenodo.org/record/4551201#.YGRXw68zY2w

https://github.com/zaneveld/GCMP_Global_Disease/tree/master/analysis/organelle_removal

My question would be how can this be converted into a fastq or .Rdata file so that it can be used as part of the IdTaxa in the dada2 pipeline that you created at the following step below:

image

I have posted the question here originally on github with the creator of dada2, Benajmin: https://github.com/benjjneb/dada2/issues/1312

Do let me know if you require more information too!

Thank you very much in advance for all your help 😁

Best Regards Aaron

DECIPHER dada2 • 44 views
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