I am processing some patient data that was generated a long time ago. Some of the files from the same sample have two different fastqs. When I ran fastqc to identify adapter content, I observed that some files are labelled as Illumina1.5 while others are labelled as Illumina 1.9 (from the same sample, from different runs).As for trimming I have to specify the phred quality in trim_galore and also HISAT2 required a flag (I haven't seen major changes when I don't put that flag, but I don't want to ignore when I have the information), I want to make sure the phred quality is really 64 or not.
However, when I look at the read quality per base. I am doubtful if the reads are really Illumina 1.5, or are just being called such.
Example. This file is being called as Illumina 1.5, but the per base quality looks similar to typical Illumina 1.9. Is this really Illumina 1.5?
Is there another way that can give me a better idea? Can I just read the top of the file and that will give me a better answer? Or shall I trust the report from FastQC?