Dear mothur users,
I am a new user of this great software. My first tests used a 454 dataset and went with no major trouble. Now I am trying to analyze a dataset from Illumina MiSeq and have difficulties.
Do you know a way to produce a single quality file (quality only or fastq, I don’t care) from two paired-ends fastq files? With “make.contigs”, mothur generates the fasta file easily, but for the qfile I have not found a solution. However, I understood from online documentation that mothur does indeed consider the quality of the forward and reverse reads to generate the contigs.
I know this is not necessary for further steps of the pipeline. However, I would like to have a look (because the samples are mixed 16S and ITS with the same barcodes, and for some samples the 16S information seems to be fine and the ITS failed, or the other way around).