I’m handling someone else project and have 9 different single-end multiplexed fastq files (actually 3 samples with 3 repeats each).
I have a metadata file- how can I import those 9 files into one qiime2 artifact file without losing the identity of each file, so I can continue with the qiime2 pipeline? I’ve tried the Casava 18 method, but since my original 9 files are not zipped it seems not to work.
This is the code I’m trying:
So that I'm 100% clear on this, you have already demultiplexed your reads in that each file contains reads that belong only to that sample? And in your case you have 3 sources with 3 samples each for a total of 9 sampling events?
If that's the case, then you should be able to use a fastq manifest file to import. You'll want SingleEndFastqManifestPhred33 as your particular --source-format. This will detect if your files are gzipped and gzip them on the way into the artifact if they aren't already.
If I've misunderstood, could you provide a screenshot of the files you are trying to import so I can get a better sense of how they are named/related? Thanks!
Thans you for the answer.
Yes- I do have 9 demultipexed files (in fasta format, not zipped) of the experiment- 3 sources with 3 samples each, for a total of 9 samples.
I’ll try the fastq manifest file method, hope it will work. I thought about using add.qiime.labels that will make me one fasta file out of the 9 files but will still keep the sampleID- but it seems not to work on qiime2.
I did tried the fastq manifest-
I uploaded all the fastq files to the directory (set as WD) with their names as written in the manifest.txt file (attached).
I ran this code, but it still not working: manifest.txt (587 Bytes)