Importing sequence reads-provenance graph

[anirban.mcgill (Anirban Kundu)]

Hi,

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

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,
Best,
Anirban

[thermokarst]

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:

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

https://dev.qiime2.org/latest/actions/transformers/

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!

[anirban.mcgill (Anirban Kundu)]

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

This forum is so cool and so helpful.

Best,
Anirban