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Rappsilber-Laboratory / xiview

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Any way to visualize linears and decoys on the public XiView? #558

Closed ciancone94 closed 9 months ago

ciancone94 commented 10 months ago

I was wondering if there was any way to visualize linear and decoy matches from a dataset on the public version of XiView. Francis informed me that the non-public version has these options. If not, are there alternatives you can think of? Such as spoofing the data that gets uploaded to XiView? I.e., listing the linears and decoys as matches in the CSM that gets uploaded.

Thanks,

Anthony

colin-combe commented 9 months ago

Hi Antony, Sorry for delay getting back to you, I was on holiday.

Francis informed me that the non-public version has these options.

Yes, the same should be available on the public version but its currently inaccessible and broken...

I'll get back to you in a day or so, cheers, Colin

colin-combe commented 9 months ago

Hi Antony,

as a quick test, if you replace the word "network" with the word "validate" in the URL you are accessing then does that page allow you to do what you want?

E.g. https://xiview.org/xi3/validate.php?upload=547-90828-08990-28852-02225

i know its not ideal having to manually change the URL,

Col

colin-combe commented 9 months ago

did this work for you? (@ciancone94 @fjoreilly )

ciancone94 commented 9 months ago

So sorry - I had seen your fix and forgot to respond. This does help me to visualize what the decoys look like, so thanks for that. Any idea how to remove consecutive peptides though? Or is this just going to be something I need to discuss with colleagues about how to script these out before loading data to XiFDR?

Thanks,

Anthony

colin-combe commented 9 months ago

Any idea how to remove consecutive peptides though?

that's currently not something you can do in the xiVIEW interface

Or is this just going to be something I need to discuss with colleagues about how to script these out before loading data to XiFDR?

there might already be options in xiSEARCH or xiFDR related to this - @lutzfischer?

lutzfischer commented 9 months ago

xiFDR has an option to ignore consecutive peptides: image

That would remove these before FDR calculation. (should be done before - otherwise the remaining result might not have the FDR you think it has)

ciancone94 commented 9 months ago

Ah, that's where it is. Okay, great, thank you.