Importing sequence reads-provenance graph


I noticed something in the provenance graph of my analysis today, I was not able to understand it-it is not an error-I would be grateful if somebody helped me with this :smile:

What does the "SingleLanePerSamplePairedEndFastq" mean? Does this mean each row is a paired sample (forward read, reverse read, sample ID?). Similar to the manifest file.

Thanks a lot,

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Hey there @anirban.mcgill! This is a great question!

Let's zoom out a bit and look at the section that these values are listed under:

Screen Shot 2020-07-10 at 2.18.21 PM

So from top down, these are the transformers invoked in the command, and specifically, this transformation was invoked on the output of the command.

So, what this is telling us is that when saving the output, QIIME 2 automatically transformed (converted) the input format (PairedEndFastqManifestPhred33V2) to the output format, SingleLanePerSamplePairedEndFastqDirFmt! Since QIIME 2 allows for multiple formats (representations, or views) of a given Semantic Type, we have the opportunity to apply various transformations that normalize or unify the data. In this case, all SampleData[PairedEndSequencesWithQuality] are internally stored as SingleLanePerSamplePairedEndFastqDirFmt - but you didn't need to know about that, or ensure that your data was formatted that way - QIIME 2 knew how to transform these data!

Hope that helps!



Thanks for the quick response Dr. @thermokarst !
Ah yes, I get it-the transformation is a mechanism for the output to be read by the developer scripts.
Wow-thanks for the link. I will read it through :slight_smile:

This forum is so cool and so helpful.



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