Hello. I have received fastq files which are demultiplexed and have already been trimmed and merged (originally paired-end). Is there a qiime2 command which I can use to create the demux.qza? I tried the cassava single lane command but I’m presuming it expects only a forward sequence.
Please let me know if I can add any clarity to my question.
Just to add on to that, set the --type to SampleData[JoinedSequencesWithQuality], it can be used with any of the single-end formats (casava or manifest-style) since the representation is the same.
Hello. I just realized that I may need a manifest file in order to use casava with joined fastq files I researched manifest file formats and could only find the following example format. If this is the correct format, both the forward and reverse sequences map to the the sample-id which seems correct. Where would I place the manifest file designation in the casava format? Thank you!
It looks like you have written out an example of a manifest file for paired-end reads. Save to a text file, let's call it pe-64-manifest. Then import with this command:
Note that I have specified as paired-end data, because it looks like you list the paired-end reads in your manifest file. If you do want to use the trimmed/joined reads as you originally declared, you can follow the import instructions given here.