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maracashay / DAWG-Helpline

Need help deciding what step to do or what specific commands to pass when analyzing your amplicon data? Ask AWAY! DAWG is here to help :)
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fastq or fastq.gz files for dada2 in R #1

Open maracashay opened 4 years ago

maracashay commented 4 years ago

Hi all,

Just to start us off, I wanted to post something that I had gotten snagged up on when I first started using dada2 in R.

You need to use .fastq files and your .fastq.gz files should NOT be in the same folder. DADA2 will give you an error when you try to read info from the .fastq files.

emilyvansyoc commented 4 years ago

Could you fix that within R by specifying the file type you're reading in with list.files()? That function takes a pattern as an argument where you could specify a regex for only fastq.

maracashay commented 4 years ago

Yes, you are absolutely right. Someone else pointed that out to me after making this post. I've since used the .fastq.gz files.