I have a FASTQ* file with reads from an Illumina machine and try to do the quality control filtering with the FASTX-Toolkit but get problems with the quality scores (see this post for a nice discussion about the scores)
fastx_trimmer run without complaining, 'fastq_quality_filter' is suddenly not happy with the files
fastq_quality_filter: Error: invalid quality score data on line 148 (quality_tok = "Z]aaaaa]O]aabaaaaa]" Petra*read2.fasta
The particular read looks like this :
@Petra_4_1_1_10_1327/1 AGTATTTTTGAATCTCATCATCGTCACTTCACTAAG +Petra_4_1_1_10_1327/1 `Z]aaaaa]O]aabaaaaa`][FW`__a`\FW_X[M
Does anyone have a suggestion (other than deleting this read) or some experience?
*well it is labeled .FASTA but looks like a FASTQ file