Benjamin Callahan

> Does this still follow with it just being off-target amplification? Thanks! Yes. Short off-target amplicons will end up in the final ASV table as being the length of the...

You can download different reference datasets, including different versions of the Silva database, that are curated and formatted for the `assignTaxonomy` function in DADA2 here: https://benjjneb.github.io/dada2/training.html The links in the...

You can make any kind of fasta file you might imagine using regular R manipulations of the sequence table and the `writeFasta` function. For example, in order to get a...

Do you get this error with the following? ``` library(ShortRead) fn

@M1chibata To troubleshoot this you'll want to isolate a single fastq file (rather than a collection) that might be causing this issue. That is, for what single file `fn` does...

The fasta file isn't in the expected format, not sure how else that error could arise. Have you opened it up in a text editor for close inspection? Were any...

Does `microseq::readFastq` handle fasta files?

First, are the primers sequenced here? In the most common V4 16S libary setups they aren't. If they aren't you should not be removing any b ases from the start...

> I also checked to see if there were primer hits in the raw reads I received, and there were (first table in my post). When I trimmed left by...

lima performs demultiplexing of the reads into the samples they came from using barcodes attached to the sequences. It also trims the barcodes. `removePrimers` then filters the read set down...