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Josh Goodman
@jogoodma
Yeah, the dojo declare is what I was referring to.
In any event, thanks a bunch. This is more than enough to get me started.
Colin Diesh
@cmdcolin
:+1:
Ian Holmes
@ihh
@jogoodma glad we could help! would be very interested to see what you do with this. As @cmdcolin mentioned, we have been extending our analytics framework recently, trying to instrument the code more carefully to model user behavior better. It would be great to develop a good data resource around this and we could potentially partner up with you if this is something you are interested in as well.
@scottcain I just saw your comments from yesterday about using NextStrain data from UCSC. Bit concerned about the idea of "liberating" GISAID data, and similarly about the idea of using UCSC bandwidth. Is there any way to do what you want to do while bypassing these issues? e.g. something you could do is not distribute the data yourself, but include a README that describes how to get it?
Scott Cain
@scottcain
@ihh I’m a little less worried about UCSC’s bandwidth after @cmdcolin pointed out this entry in the FAQ: https://genome.ucsc.edu/FAQ/FAQdownloads.html#download2
I think that entry is for tools like IGV that might be pulling data directly from UCSC, but applies equally well to JBrowse. Additionally, I really doubt they’d notice a blip of increased bandwidth utilization from JBrowse users.
Scott Cain
@scottcain
@cmdcolin was there something done in the code base or by locally by me to allow the y axis to be not “pretty” (ie, I can set them to 4.25 if I want and JBrowse won’t round it to 5)? I remember addressing this a while ago. Was it "fixBounds" : false?
Colin Diesh
@cmdcolin
sounds about right
fixBounds was added pretty recently i think for doing that
Scott Cain
@scottcain
yes, 1.16.2. Thanks
Scott Cain
@scottcain
I’m thinking about how I can make use of variant data in VCF where the results of the Variant Effect Predictor (VEP, Ensembl) for individual transcripts are included (so if a variant occurs in a gene with 10 transcripts, I have 10 results in that line of VCF to indicate how it affects each transcript). While I have a picture in my head, I don’t think it will be realistic to implement in JBrowse. I’m envisioning a super-glyph where it would display transcripts with the variant glyph just above (like, touching) the transcript, where I could color code the variant according to, say, severity of the effect. Potential problems include so many variants that there is just a mess (in which case, filtering would come in handy). Does this feel realistic and useful?
Colin Diesh
@cmdcolin
@scottcain does the VEP result include predictions on each different transcript?
that is interesting
Scott Cain
@scottcain
Yes
Colin Diesh
@cmdcolin
ya
i would say, megaglyph sounds cool
the display of multiple transcripts per gene is already quite space-consuming
might as well just eat up a little more space for the good benefit
Scott Cain
@scottcain
oh, yeah, that’s much better than super glyph
Colin Diesh
@cmdcolin
megaglyph vs supersprite
Scott Cain
@scottcain
And I would think of this megaglyph used in a track that is separate from a typical “genes” and “variants” tracks, so users would be turning on with the understanding that it would be a tall track.
Colin Diesh
@cmdcolin
that is probably fine
i think, even, the default behavior of jbrowse to display all transcript variants is somewhat debateable at times. that results in tall tracks very often
Scott Cain
@scottcain
right—I’m not really concerned with the vertical space it would take up.
Re: variant tracks: agreed. That’s why I’d like to see filtering with lots of knobs and switches.
Colin Diesh
@cmdcolin
technically jbrowse 1 even has a nice filtering framework. it's under utilized
Scott Cain
@scottcain
It’s also why WB has 5 or 6 variant tracks—we kind of pre-filter for typical use cases.
Colin Diesh
@cmdcolin
programmatically you can do quite a lot with it, currently its really only used to hide variants that dont pass filters
Scott Cain
@scottcain
the filtering in JB1 needs a UI
more expressive ui
Colin Diesh
@cmdcolin
its a little bit hard to make such a general thing have a ui
Scott Cain
@scottcain
For sure
Colin Diesh
@cmdcolin
i proposed having bcftools filters recently https://samtools.github.io/bcftools/howtos/filtering.html which i think are quite powerful, and are flexible text expressions. slightly cryptic but powerful in the right hands
Scott Cain
@scottcain
“slightly cryptic” lol
But yeah, that would be cool
Colin Diesh
@cmdcolin
its as cryptic as the command line is cryptic, which really is not very
Scott Cain
@scottcain
Having never used it, I just glanced at your link and thought “no way an ordinary user is doing that"
Colin Diesh
@cmdcolin
looking at command line interfaces have the same effect on many people
but in general they are one of the most powerful tools for analysis
Scott Cain
@scottcain
of course.
Scott Cain
@scottcain
@cmdcolin just now, on dev branch: TypeError: this.config.replaceRefRename is not a function at http://18.212.36.249/jbrowse/?data=data%2FSARS-CoV-2&loc=NC_045512.2&tracks=DNA
in jbrowse.conf replaceRefRename = nc_045512v2 customRefRename = nc_045512.2 which I assume is the appropriate syntax
Colin Diesh
@cmdcolin
@scottcain the syntax is customRefName=function(refname) { return refname==='nc_045512v2'?'nc_045512.2':refname }
they are callbacks
customrefname is to add to the custom refname renaming logic
replacerefname is to fully replace the refname renaming logic
Scott Cain
@scottcain
Oh, that’s much better—I was wondering how you’d handle something more complicated that a single substitution. The other thing that tripped me up momentarily was the misnaming of the parameter (you gave customRefName but it’s customRefRename)
Colin Diesh
@cmdcolin
:{
Scott Cain
@scottcain
In the release notes it’s right, it was just above ^^ that it was off. It didn’t take me too long to catch :-)