how do I import single reads only if I have paired-end data?

Sorry again,

I need help (anyone!) importing paired-end data as single end, I did
qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path its-obj1 --input-format CasavaOneEightSingleLanePerSampleDirFmt --output-path qiime-forwardreads-obj1/demux-singlefoward.qza

But got error
There was a problem importing its-obj1:

/tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-eo6_8gwa is not a(n) SingleLanePerSampleSingleEndFastqDirFmt:

Forward and reverse reads found.

I have been reading other related posts in the forum trying to understand how to solve the challenge but cant seem to wrap my head around it.

How do I import forward/reverse reads only into a qiime artefact?

Thank you in advance for your patience and understanding.


Hi @anethdavid,

This varies by the type of import you are using. With Casava 1.8 (the format you are using), you will need to make a new directory and copy over only the forward (or reverse) fastq files. Alternatively you may find it easier to use a single-end manifest format, which will allow you to specify the location of individual files that you wish to import.

Good luck!


Thank you for the response, I copied forward and reverse reads into separate directories and imported with Casava 1.8 single end, it worked!

Thank you very much!


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