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Sorry if this is a silly question but I wanted to know what parameters the pipeline chose to filter the "filtered-table.qza". When I look at the output files on the nexflow ampliseq github page under …
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Hi,
I'm running this on HPC with singularity. I can't tell what caused this termination at the denoise step. I was following the documentation and everything before the test sample step works fine…
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Hi! I have run the ampliseq pipeline before on an older macbook without any problems, but now I'm tryin to run it on a newer computer equipped with an Apple M1 processor and it seems to be running int…
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Hi!,
Can you please help me get more information about mp_cal_venn and mp_plot_venn?
I am building my Venn diagrams using the following commands:
>r.Venn.12 % mp_cal_venn(.abundance=RareAbundan…
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Hello
I have noticed recently that rarefying the phyloseq object directly root the tree.
`ps.3.rare
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Hello,
I am referring to section 4.9.4 estimation of the core/pan-genome size by sampling genomes. I created the estimated core genome size graph for 4 species. However, there appears to be core g…
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```
remotes::install_github("Arcadia-Science/sourmashconsumr")
library(sourmashconsumr)
library(dplyr)
library(ggplot2)
library(purrr)
sigs %
map_dfr(read_signature) %>%
filter(ksize == …
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Hi,
I am testing the AMR++ with heavier data but I fails due to an error on trimmomatic. The output of trimmomatic.stats.log is below. It seems that it did not find any clipping sequence and ends.…
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Hi!
I'm trying to use gllvm to look at differences in species composition of the gut microbiome. I have fit the null model using negative binomial distribution and using 3 latent variables. I then …
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I would like to analyze the FASTQ output using my own guppybasecaller GPU instead of the MetONTIIME pipeline.
Is it necessary to pre-process the reads with Nanofilt (e.g. remove reads less than 500 b…