New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Can't load specific bigbed file from UCSC #1226

cmdcolin opened this Issue Oct 5, 2018 · 1 comment


None yet
2 participants
Copy link

cmdcolin commented Oct 5, 2018

The file from isn't able to load and has infinite loading bar in JBrowse

I don't think there's anything particularly weird about this file, it just looks like this

chr1    0   3782    AKR_J   0.773556
chr1    0   3782    C3H_HeJ 0.771731
chr1    0   3782    CBA_J   0.775481
chr1    0   4790    A_J 0.677822
chr1    122 4790    C57BL_6NJ   0.653361
chr1    122 4790    NOD_ShiLtJ  0.630747
chr1    136 3782    DBA_2J  0.757485
chr1    158 2559    WSB_EiJ 0.464704
chr1    158 4790    129S1_SvImJ 0.578083
chr1    158 4790    CAST_EiJ    0.535326
chr1    158 4790    LP_J    0.578083
chr1    158 4790    NZO_HlLtJ   0.65974
chr1    158 4790    PWK_PhJ 0.557667

track config


This comment has been minimized.

Copy link

cmdcolin commented Oct 5, 2018

If I re-encode the file using

table scores
"custom track types"
string  chrom;          "Reference sequence chromosome or scaffold"
uint    chromStart;     "Start position of feature on chromosome"
uint    chromEnd;       "End position of feature on chromosome"
string  name;           "Name of gene"
double    score;                "Score"

And run through bedToBigBed -type=bed3 data.bed chrom.sizes then the features do load. It is maybe an issue that I can't read the native bb file that is on their server though

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment