Dear Qiime community and forum maintainers,
I am here contacting you with a request similra to the discussion from Merging paired end sequences after importing fastq manifest data. I have worked with Qiime 1.9, and only now start using Qiime 2 (installed 3 days 15.11.2017
My questions are below this following block and here is what I did:
I downloaded demultiplexed (i.e. one file per sample) forward and reverse
.fastqfiles from Illumina basespace.
I created a manifest file called 05_manifest.txt (13.6 KB) which seemingly won't hold more then the three required metadata columns.
qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]' --input-path "$trpth"/"$inpth" --output-path "$trpth"/"$otpth" --source-format PairedEndFastqManifestPhred33which worked fine.
As my samples are already demultiplexed I called, as suggested in referenced thread,
qiime demux summarize --i-data "$trpth"/"$inpth" --o-visualization "$trpth"/"$otpth"which worked fine.
I would be happy if you could assist with the following questions:
- How do I remove adapter sequences and primers, if I am skipping the demultiplex step? I am assuming they would still be in there.
- How can I feed my sample metadata information (a.k.a "mapping file" contents) "into Qiime", if this is normally done also at the demux step.
I would be looking forward to hearing from you in due course. I have screened other replies but could not find any answers specific to this question.
Python version: 3.5.4
QIIME 2 release: 2017.10
QIIME 2 version: 2017.10.0
q2cli version: 2017.10.0