Support for unstranded data

It seems that the v0.1 milestone will support only stranded data.

We need to make sure that in later versions we support unstranded data as well.

added Won't fix label

It seems that we might not support it in the end, so closing for now.

closed

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I disagree strongly and think it should be part of the published version. The very first test with external real-world data (SARS-related samples) demonstrated that there are still plenty of relevant unstranded libraries around. Besides, whether a library is stranded or not is not something that is (unfortunately) typically reported when uploading samples to SRA, so whenever anyone wants to run any sample from there, it's a gamble we will accept it (after checking first with another pipeline) or not. That's a really poor user experience...

Well.. I think the generating unstranded data makes no sense, especially now. When analyzing such data people make choices that are not warranted and introduce errors for sure (e.g. cumulating reads from plus and minus strand, and of course, discarding regions where there is transcription in both directions. I don't want to spend time implementing and testing choices like this. How do you want to proceed?

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reopened

I understand the sentiment but then that argument applies more or less to any data that were obtained with inferior protocols or outdated technology. And to my taste that depends a little bit too much on personal opinion and what kind of resources you have access to. Unstranded data has been proven useful in the past, so I can't really see how analyzing them makes no sense, despite all the obvious drawbacks.

Anyway, how about we leave this issue open and defer the discussion until we know how to proceed with Rhea? If we want to allow our users to analyze samples straight from SRA, I think Rhea should handle the vast majority of samples on there, and that would probably mean it should handle unstranded libraries. If we don't care too much about that particular use case and mostly concern ourselves with how Rhea can serve ourselves, then we should probably drop it for the reasons mentioned.

This feature will not be implemented in the near future according to our scope. If the public requires it we can implement it in later versions.

closed

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reopened

changed milestone to %pipeline

added Discuss Future labels and removed Won't fix label

Do if reviewers ask for that, otherwise wait until users ask for it

closed

removed Future label