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joey711 / phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
http://joey711.github.io/phyloseq/
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working with phyloseq with MG files #884

Open atarauzan opened 6 years ago

atarauzan commented 6 years ago

Hi I have fastq files of metagenome seq, I also have the whole genome of specific bacteria, I want to know if phyloseq can work with this kind of data. Thanks Atara

colinbrislawn commented 6 years ago

Hello Atara,

Phyloseq was designed to work with 16S amplicon data. Have you considered trying metagenomeSeq? This is the spiritual predecessor to phyloseq, and it was designed to work with more types of data, and it might be a great fit for you.

Colin

P.S. If this answers your question, feel free to close this issue.

cjfields commented 6 years ago

Just as a note, I have used phyloseq with metagenomic data generated as output from MEGAN, where taxonomic and functional abundance is estimated from alignment. It works fine though I'd suggest it's worth keeping in mind the methods used for taxonomic assignment (essentially BLASTX against the NCBI nr protein database) have their own questions associated with them.