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Hi Anna and co-authors,
Thanks for the wonderful work on this pipeline - it's really a great resource for the whole community.
**Q/request**: I am interested in using dadasnake for doing paramet…
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I have the .fastq files for the F and R sequences that were processed and merged but would like to test if I will get the same results as the one I did with the dada2 pipeline but cannot figure it out…
seqlt updated
2 months ago
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Hello,
I am losing a lot of reads at the filtering step of dada2 for one of my runs. After reading issue #1133 it seems this is okay.
However, I want to analyse two runs together. One run loses a l…
DCHed updated
1 month ago
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I have a problem with **dada2** rebooting my system when trying analysis with the **PR2** database.
My system info:
OS: Ubuntu 23.10
Hardware: HP HP EliteBook 840 G4
Processor: Intel® Core™ i7-7…
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Hey all,
I am new to phyloseq and have a question about loading taxonomy in the package. I have created an ASV table using the dada2 ITS pipeline workflow [https://benjjneb.github.io/dada2/ITS_work…
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This lesson is meant to be a bit modular, so that it can be adapted to a few different workflows depending on user preference. That said, we do need a default one. Here are my thoughts:
**OTUs vs. …
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Hello!
I'm analysing the trunk's microbiome of a tree (MiSeq 16S V4). Since it's woody tissue, is expected to have very low diversity, therefore, my ASV abundance table has samples with very low fe…
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Currently, the pipeline uses NCBI's `rankedlineage.dmp` taxdump file for taxonomic standardisation, which only has the ranks `kingdom`, `phylum`, `class`, `order`, `family`, `genus` and `species`. How…
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Dear Amy Sweeny,
I read your great paper ... Please you can help me to fit a model.
I have this variables:
asv : DADA2 output
treat : 3 differents (class1, class2, class3)
time : 3 diff…
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I am new to microbiome data analysis
I am trying to use DEICODE to generate distance matrix.
Is there way to convert otu_table generated by R and dada2 pipeline otu_table (as qza file formate …