do I understand correctly that you just add the coding that you know your .qual file has as a format= parameter for make.fastq command.
For example I have illumina 1.8 quality scores Ill put make.fastq(fasta=a,fa,qfile=a.qual, format=illumina1.8), if solexa then format=solexa.
The format parameter is NOT to convert from one format to another etc?
edit: a feature request - several programs and databases accept also space delimited decimal quality scires for fastq qaulity format. maybe add that format too
You are correct the format parameter is used to tell mothur what format your fastq files are in. Mothur uses this information to properly translate the quality characters to scores.
So if I happen to have quality scores that are just pure Phred (an output from a bioinformatic program). Then should I convert them before using make.fast format=sange by shifting the values up by 33?.
Using the default/sanger format: right now if I enter my values as they are then my Phred score of 40 will be convertedto I=(phred score of 72 sangfer score of 40) - which seems to be all-ready correct approach? If I’d pre-convert them they would be presented as too large?