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igvteam / igv.js

Embeddable genomic visualization component based on the Integrative Genomics Viewer
MIT License
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ChromHMM tracks #961

Open Parul-Kudtarkar opened 5 years ago

Parul-Kudtarkar commented 5 years ago

Can igv display chromhmm tracks such as the ones in this example

http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr12%3A56694976%2D56714605&hgsid=751999545_9P4Dy9wrRAaQSt8daXMlEH4VrwMb

thanks!

jrobinso commented 5 years ago

No it can not. What is the file format for this data?

Parul-Kudtarkar commented 5 years ago

either bigBed or bed For example - https://www.diabetesepigenome.org/search/?type=Annotation&files.file_type=bed+bed3%2B&files.file_type=bigBed+bed9&annotation_type=chromatin+state

jrobinso commented 5 years ago

Well bigbed and bigwig are supported, but it will not look like the tracks you linked to.

Parul-Kudtarkar commented 5 years ago

Thanks @jrobinso! Yes, they do load without any issue. I hope a feature supporting chromhmm files would be great to have for igv

jrobinso commented 5 years ago

We'll leave this open.

jrobinso commented 3 years ago

see https://genome.ucsc.edu/cgi-bin/hgTrackUi?g=wgEncodeBroadHmm&db=hg19