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zavolanlab / htsinfer

Infer metadata for your downstream analysis straight from your RNA-seq data
Apache License 2.0
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Create overview figure panel #155

Closed uniqueg closed 5 months ago

uniqueg commented 6 months ago

Create high level ("graphical abstract") overview of what HTSinfer does, in vector graphics.

balajtimate commented 6 months ago

htsinfer_workflow_overview Would something like this work?

uniqueg commented 6 months ago

This is great - thanks a lot @balajtimate!

The only thing I'm not sure about is the tool names in the blue boxes. What do they signify? Do we use kallisto to "infer" the library source, STAR for the read orientation and Cutadapt for the 3' adapter sequences?

uniqueg commented 6 months ago

And perhaps about the pictograms:

balajtimate commented 6 months ago

Do we use kallisto to "infer" the library source, STAR for the read orientation and Cutadapt for the 3' adapter sequences?

Yeah, exactly. Technically, STAR is also used for library type inference when the seq_ids are not present, but for the read orientation it's always used, so for the overview I think it's enough to put it there. If the flow is not obvious, I could put some arrows to indicate it more visibly.

The library type isn't very obvious. Might be better to have something that indicates single vs paired. Not sure what though.

Yeah 😅 Maybe a single and double arrows from the read orientation pictogram, and for that, add another pair of arrows showing the forward read as 2, and reverse as 1?

so perhaps increase the letter sice a bit and then use only one row?

Sure, I'll change that.

uniqueg commented 6 months ago

Yes, good idea about the library type pictogram.

I would probably put STAR in as well for the type inference, but maybe with a slightly in a lighter blue shade or with a pair of brackets around it? Just for completion.

Also, how is Cutadapt used for the 3' adapter sequence? I thought Rohan implemented some fancy search algorithm for that. Sure Cutadapt isn't just used for polyA tails?

balajtimate commented 5 months ago

Here is an updated version: htsinfer_workflow_overview

uniqueg commented 5 months ago

Great! I think you can just attach the SVG file as well here, then close the issue :)

balajtimate commented 5 months ago

Here is the SVG: htsinfer_overview_figure