I am trying to use QIIME 2 2018.4. When I import fastq data my csv manifest file is not working. How can I make my own manifest file as the example of “pe-64-manifest”
Create preliminary manifest file (sample ids will be missing)
DO NOT RUN THIS UNSEEN AND DO MODIFY THIS ACCORDING TO YOUR NEEDS.
- create first file path dump for manifest file
find /path/to/data -type f \( -iname "*.fastq.gz" \) >> /path/to/manifest_prelim.txt
forwardstring to manifest:
sed -i '/_R1.fastq.gz/ s/$/,forward/' /path/to/manifest_prelim.txt
reversestring to manifest:
sed -i '/_R2.fastq.gz/ s/$/,reverse/' /path/to/manifest_prelim.txt
- replace double slashes string in manifest:
sed -i 's&//&/&g' /path/to/manifest_prelim.txt
After this add header to file, and add the sample ids, before the sequences. Also check all samples are there, and all files are in pairs.
Results may vary (also based on
sed syntax). Please create backup copies of your data etc. and please note that I am not affiliated with the Qiime developers.
would you mind posting your manifest.csv. It may be a syntax thing
in addition to sharing your manifest file, please also share the error that you are receiving. Have others reported this error on the forum?
An off-topic reply has been split into a new topic: EOFError: Compressed file ended before the end-of-stream marker was reached
Please keep replies on-topic in the future.
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