qiime2 paired end fastqs import

Question

[10mz1]

Hi all,

I'm trying to import data into Qiime2. This process seems convoluted and complicated. i've tried importing in several ways but the software does not play nice with paried end reads. therefore i have followed their instructions for creating a manifest file, to tell the software how to import the reads. now i am getting errors and am unsure of what 'type' the fastq files are, for example the software demands very specific type of fastqs for importing eg Phred33V2, Phred64V2, etc. How might I know what type of fastq files I have? Is there any guarantee they are one of these types?

Answer 1

[GenoMax]

Recently produced data should be using Sanger encoding (Phred33V2). You can always test your files using testformat.sh from BBMap suite to be sure.

$ testformat.sh in=file_2.fastq
sanger  fastq   raw     single-ended    76bp