Importing single end read (forward)


I was unsuccessful to import the single end read. I have error in either --type or --input-format I suppose.

I checked the qiime tools import --help, first.

Second, I visit the web site.

and finally I reviewed this page:
Importing data — QIIME 2 2019.1.0 documentation

But I did not understand what is the problem rooted in! i have some doubts on type and input-type.

First of all, please tell me how can I find the types scripts for single- and paired-end reads.
Lastly, what is the problem in your idea? How can I overcome that?



Hey there @Mehrdad!

Thanks for doing your homework!

You are correct! The problem lies in the type you specified — for single end you should use type MultiplexedSingleEndBarcodeInSequence. Also, no need to specify the format, since that format is the default format for this type. So, your new command should look like this:

qiime tools import --type MultiplexedSingleEndBarcodeInSequence --input-path Forward --output-path ImportedonlyforwardlibA.qza

Ah, this is a hard one right now, we still haven’t built our docs listing all of these types and formats. The best we have right now is

qiime tools import --show-importable-types
qiime tools import --show-importable-formats

Thanks you dear admin!
It is done successfully!


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