nhg12

It gives this error: Error in table(otu_table$batch - column) : object 'column' not found

This is what I have been doing so far: ##load data in R## I've converted the BIOM ASVs file form QIIME to TSV and then to csv to load in...

phyloseq-class experiment-level object otu_table() OTU Table: [ 8397 taxa and 1 samples ] sample_data() Sample Data: [ 1 samples by 2 sample variables ]

HI So the files that I upload have all the samples. I then do this: count_tab

hi @effelsbn I see that you had your problem solved. I am having a similar problem. Can you please share the parameters you used to resolve the issue? Was it...

Hi @benjjneb @effelsbn @cjfields for your quick replies. I was actually doing the analysis in QIIME2 and now would give it a try in R for more flexibility. I am...

I tried setting max-ee to 10 and 20 and still 60% of my reads are getting filtered. I don't understand why my sequences are getting filtered when they are high...

No QIIME2 shows initial quality of the data and then the final stats after DADA2 pipeline. The length of my sequences is ~1550 bp after primer removal. Get Outlook for...

Now i ran one sample through R DADA2 pipeline so I could change some more parameters, Tis is what I ran:track

We used PacBIO sequel II. These are skin swab samples