Changing Whacky Fastq Quality for Demultiplexing
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
1 answer
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" :-)
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If you want to change the quality scores you could use
reformat.shfrom BBMap suite like so:reformat.sh in=your.fq out=changed.fq qfake=29.