This is a typo right, dada2 truncate?

From dada2 plugin, in both single and paired end

--p-trunc-len-r INTEGER Position at which reverse read sequences
should be truncated due to decrease in
quality. This truncates the 3' end of the of
the input sequences, which will be the bases
that were sequenced in the last cycles.
Reads that are shorter than this value will
be discarded. After this parameter is
applied there must still be at least a 20
nucleotide overlap between the forward and
reverse reads. If 0 is provided, no
truncation or length filtering will be
performed [required]

Shouldn't this say reads that are longer than this value will be discarded? Unless I am totally missing something here... This has led to a lot of confusion for me, but it appears this is just a typo, and looks like it starts as a typo in dada2.

Hey there @CarlyRae, no, this isn’t a typo — by definition you can’t truncate something shorter than the desired truncation length. This is why DADA2 discards any reads shorter than the truncation length. So think of it this way:


If I specify a trunc-len of 5, the first sequence will be truncated to AAAAA, while the second one will be dropped entirely, because it is shorter than the specified trunc-len. Make sense?

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It sounds like you might be confusing “discarding” with “removing nucleotides” here — discarding in this case means dropping the entire read, while truncation refers to removing the nucleotides past a certain position.

Ah yes, I was totally misinterpreting what it was saying.

Any reads that are shorter than this value will be discarded. The remaining reads will be truncated at the 3’ end to the length of this value.

Your example was very helpful.


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