after a very disillusioning experience with the moving-pictures tutorial, again I’m facing issues with the importing data tutorial, part Casava 1.8…
The browser download creates a new and unzipped folder “casava-18-single-end-demultiplexed” in my Downloads and this folder contains 138 fastq.gz files.
Because the tutorial says “save as .zip” I tried to zip the folder by
zip casava-18 zip error: Nothing to do! (casava-18.zip)
Which means to me, that obviously the folder is zipped somehow.
So, I proceeded with the tutorial:
unzip -q casava-18.zip unzip: cannot find or open casava-18.zip, casava-18.zip.zip or casava-18.zip.ZIP.
unzip -q casava-18
Because the folder obviously is not zipped, I hoped for the best and ran the code:
qiime tools import \ --type 'SampleData[PairedEndSequencesWithQuality]' \ --input-path casava-18-paired-end-demultiplexed \ --input-format CasavaOneEightSingleLanePerSampleDirFmt \ --output-path demux-paired-end.qza
and tadaaa! Worked!
Now I wanted to see demux-paired-end.qzv by
qiime demux summarize \ > --i-data demux-paired-end.qza \ > --o-visualization demux-paired-end.qzv
Press the ‘q’ key, Control-C, or Control-D to quit. This view may no longer be accessible or work correctly after quitting.
So, I have to quit the whole qiime session every time, I want to see the results? Is that normal?