I have some RNA-seq data and FastQC says some of the files have quality scores encoded with "Illumina 1.5" and some with "Sanger / Illumina 1.9". HISAT2 has the option to specify --phred33 or --phred64. I think Illumina 1.5 is phred64 and Illumina 1.9 is phred33, is this correct?
For consistency in running my analysis pipeline I'm considering converting the 1.5 files to 1.9 before alignment, would this be a good/bad/neutral idea and what is a good tool to do this?
For consistency in running my analysis pipeline I'm considering converting the 1.5 files to 1.9 before alignment, would this be a good/bad/neutral idea and what is a good tool to do this?
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