Expected error filtering on Ion Torrent data using fastq_filter USEARCH command

Question

[sukhu.sakhare]

Hello, I am doing 16s rRNA analysis on Ion Torrent data using Usearch pipeline. I got error at quality filtering step. Command used for the quality filtering is:- usearch -fastq_filter Reads_trunc.fq -fastq_maxee 1.0 -fastaout Reads_filtered.fa

Error got is:- "CharToIntQual('L') Phred score 43 out of range 0..41"

I have changed the -fastq_maxee value to 0.5 but still got the same error. I can't figure out the reason behind the error. Need help

Thanks in advance.

Answer 1

[Simply Bioinformatics]

USEARCH Fastq-Filter for Ion-Torrent 16S
usearch -fastq_filter in.fastq -fastqout out.fastq -fastq_ascii 33 -fastq_qmin 0 -fastq_qmax 47

Answer 2

[Brian Bushnell]

The problem is that the quality scores are out of the expected range. Before you can proceed further, you need to figure out why that is the case. For example, they may have been incorrectly processed, the file may be corrupt, or it may be that they are actually not Ion Torrent reads but very old Illumina reads. I am not familiar with Ion Torrent data so it could be that 43 is a normal quality score for it, in which case you might need to restrict the range to 0-41, which you can do with BBMap's reformat.sh. But first find the reason why you have a base with Q43.

[sukhu.sakhare]

Thank you for your suggestion. I have used -fastq_qmax parameter and it worked. Thank you