This is a test version of Biostars. For the public version, visit https://www.biostars.org.
qiime2 paired end fastqs import

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?

qiime2 metagenomics
• 1,389 views • link
updated by GenoMax GenoMax • written by 10mz1 • 10mz1

1 answer

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
• 0 views • link
written by GenoMax GenoMax

Log in to answer this question.

More posts like this