Why does my stability file look like this?
make.file(inputdir=/Users/meghanstern/Desktop/mothur 2.0,type=fastq, prefix=stability)`````
This is the only code I used so far. I was trying to follow the MiSeq SOP but I can't make contigs.From the looks of the error message in the background, it appears that you only have one fastq file in the directory and that it doesn’t have a pair. Also, I’d strongly encourage you to get ahold of a text editor like Virtual Studio Code (free!) to look at text files. Using MS Word will cause you a lot of pain for these applications in the long run.
pat