bam file won't display - Githubissues

g2nb / igv-jupyter

Extension for Jupyter which integrates igv.js

MIT License

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bam file won't display #33

Closed njbernstein closed 4 years ago

njbernstein commented 4 years ago

Hi there,

Trying to track down why my bam wont display, and I don't get any errors from IGV. Screen Shot 2020-01-27 at 11 34 00 AM

Nothing returns. any help would be much appreciated.

jrobinso commented 4 years ago

I suspect its the bam path. If you can use Chrome or some other browser with "devtools" look at the url that path is resolving to.

hurleyLi commented 4 years ago

Hi, I'm having the same problem. Everything is installed and enabled, and I got a confirmation when I launched jupyter lab igv enabled!. But nothing happened when I run code similar to above, and there's no error message either. Do you have any idea what might cause this? Thanks!

jrobinso commented 4 years ago

Hi, first igv-jupyter does not support jupyter lab, did you mean jupyter notebook?

njbernstein commented 4 years ago

My issue was dumb I needed to use the full like so: bam_path = "http://sci-pvm-nicholas:10000/tree/projects/genomics/ukbb/ch/data/siddhartha_2017_subset_crams/5989838_23163_0_0.subset.sorted.bam"

jrobinso commented 4 years ago

@njbernstein Ah ok, thanks for letting me know. There is a way to use relative paths for files using "file magics". I do python so seldom the details escape me, but I did get it to work once.

hurleyLi commented 4 years ago

working now after switching from lab to notebook. Thanks!