Hi Technical pals,
Please make bold or highlight where in commends should be changed by users, and put their info in the text of parameters. For example in this command:
qiime demux emp-paired
–m-barcodes-file sample-metadata.tsv
–m-barcodes-column BarcodeSequence
–i-seqs emp-paired-end-sequences.qza
–o-per-sample-sequences demux.qza
–p-rev-comp-mapping-barcodes
qiime demux summarize
–i-data demux.qza
–o-visualization demux.qzv
I am not sure I did correctly above or not, but without bolding there is a big problem for novice like me!
As you know, in Linux which is sensitive to Lowercase, capital, dot, without and so on, so it is better to make comfortable condition by doing the simple thing.
Another problem:
Regarding de-multiplexing paired-end data, there is no a fixed command like EMP. A user how should do that while there are a lot of options in there. In EMP demultiplexing step, you provided a command. By coping that and changing some parameters it is easy to run that command while in paired-end I faced with problem. I put slashes between the arguments, not worked! Please visit the following link and give me a feedback:
https://docs.qiime2.org/2018.2/plugins/available/cutadapt/demux-paired/
Thanks a lot