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GMOD
JBrowse 1, a full-featured genome browser built with JavaScript and HTML5. For JBrowse 2, see https://github.com/GMOD/jbrowse-components.
There are concerns often about the size of the index file e.g. #542 htsget provides a way to query NGS data without parsing bam/cram index files
Currently I have a massive GFF file containing a lot of redundant and insignificant protein sequences to my project. It would be extremely efficient if I could view this GFF...
Just like [GGB ](http://gmod.org/wiki/GBrowse_2.0_HOWTO#Track_Definitions) > Simply provide the feature option with a space-delimited list of the features you want to include. For >example: > >feature = gene:sgd stRNA:sgd it's not...
If a feature is of type mRNA or gene, show a special detail dialog that has features optimized for genes. Including: - CDS sequence - toggle introns on/off - functional...
Supporting a GFF file like this: ``` 1 araport11 mRNA 52061 54689 . + . ID=transcript:AT1G01110.1 1 araport11 exon 52061 52730 . + . Parent=transcript:AT1G01110.1;Name=AT1G01110.1.exon1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01110.1.exon1;rank=1 1 araport11 five_prime_UTR 52061 52730...
We regularly set chunkSizeLimit appropriately on BAM tracks with no problems but I've recently discovered that changing the value via the track menu and 'edit config' doesn't seem have an...
When using biod-to-json.pl to generate data from a Chado database, the script generates multiple features for a gene when that gene has several associated analysisfeatures. Is there a way to...
Hello, When chromosome Name and ID differ in GFF3 file, using biodb-to-json.pl results in tracks containing no data in JBrowse. We discovered this issue by trying to use GBrowse's yeast...
In large installations like @scottcain manages, when there are huge numbers of configuration files that are imported into each other using `include`, the initial JBrowse load can be quite slow,...
It was noted that sometimes when opening a popup (in jbrowse...) it will automatically scroll to the bottom. First discussed here http://gmod.827538.n3.nabble.com/Gmod-ajax-JBrowse-Popup-focus-td4053110.html I had also noticed this for awhile but...