How to generate qfile for joined paired-ends reads?

Commands in mothur
1

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).

Yours,
Maxime

2

The next release will output the quality scores; however, it is unclear what one would do with the quality scores at this point.

Pat

3

Your answer seems to confirm that this is not possible now. As I wrote in the initial post, this was just for curiosity’s sake. I am eager to see the next release.

Thank you for your help,
Maxime

4

Pat, I realized that I could also do the quality control of my sequences before having mothur assemble the contigs. But then it will likely occur that only one sequence of a pair is deleted (due to unsufficient quality) and the other one is retained. Will mothur manage this?

Yours,
Maxime

5

mothur is not set up to do this. in our experience the approach taken in make.contigs gives better results than trimming and then assembling.