In the documentation for the core arguments it says that for -A/--asvs path, the "...file must contain some unwanted length variants."
Reading through the length-based arguments documentation, this requirement didn't really become clear to me.
I am working with the regular 313 bp fragment used for COI metabarcoding and have filtered my reads in dada2 to only retain the ones with a sequence length of 313 (the stringent setting is a bit of a special case, as I want to use the sequences for metaphylogeography). Can't I just set the same value for n and x (313) in -n/--minimumlength n and -x/--maximumlength x, to fufill the requirement of having to set a value here? And why do I need an input file of sequences with length variation?
Hi @tjcreedy
In the documentation for the core arguments it says that for
-A/--asvs path, the "...file must contain some unwanted length variants."Reading through the length-based arguments documentation, this requirement didn't really become clear to me.
I am working with the regular 313 bp fragment used for COI metabarcoding and have filtered my reads in dada2 to only retain the ones with a sequence length of 313 (the stringent setting is a bit of a special case, as I want to use the sequences for metaphylogeography). Can't I just set the same value for n and x (313) in
-n/--minimumlength n and -x/--maximumlength x, to fufill the requirement of having to set a value here? And why do I need an input file of sequences with length variation?Thanks Nauras