Changing Whacky Fastq Quality for Demultiplexing

Question

[zach]

Hi all.

I am using Qiime2 to demultiplex a paired-end sequences with a barcode. Unfortunately, my barcodes.fastq file has really weird quality score for its 4th line (only with '@'). Qiime2 cannot demultiplex with such faulty scores.

Is there a way I could change the quality score? Otherwise, how could I demultiplex my sequences whilst disregarding the quality scores?

Cheers!

Zach

[GenoMax]

If you want to change the quality scores you could use reformat.sh from BBMap suite like so:

reformat.sh in=your.fq out=changed.fq qfake=29.

Answer 1

[Gabriel R.]

Can you try deML? It is a maximum-likelihood demultiplexer (see our paper in Bioinformatics). If you have a '@', it means a QC score of 31 which is not too far off the "normal" error rate for Illumina data? BTW, your question should not be a "forum" :-)