I am having trouble importing my fastq file into QIIME2. My manifest file seem to be correct but I have read about invisible things in the file that can affect things and I do not know how to find the invisible characters.
Can someone help me please?
Here is the code I am using:
qiime tools import
--type 'SampleData[SequencesWithQuality]'
--input-path /igbgroup/n-z/valizad2/Dissertation_Pilot/Microbiome_Analysis/20181012-PrimerSorted-Manifest.csv
--output-path 20181012-single-end-demux.qza
--input-format SingleEndFastqManifestPhred33
and here is the error:
There was a problem importing /igbgroup/n-z/valizad2/Dissertation_Pilot/Microbiome_Analysis/20181012-PrimerSorted-Manifest.csv:
/igbgroup/n-z/valizad2/Dissertation_Pilot/Microbiome_Analysis/20181012-PrimerSorted-Manifest.csv is not a(n) SingleEndFastqManifestPhred33 file
Hey there @Negin! We need a little more information in order to help you --- can you please share your manifest? Feel free to send to me in a private message if you need to keep these data private.
Thank you for your reply. I was able to read in the sequences. I was using the wrong method. This is what I used and it worked. I just had to zip my file first. I am just wondering why we can't use this method for unzipped files because none of the other methods works for me.
