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Shians / NanoMethViz

Apache License 2.0
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How to use own annotation? #3

Open JWDebler opened 3 years ago

JWDebler commented 3 years ago

How can I use my own gff or gtf gene annotations files? The vignette only mentions a way of importing annotations from another package.

Shians commented 3 years ago

I may try to add tools to help with this in the future, but you can use any annotation that has the following columns

   gene_id   chr   strand    start      end transcript_id symbol
   <chr>     <chr> <chr>     <int>    <int>         <int> <chr> 
 1 100009600 chr9  -      21062393 21062717         74536 Zglp1 
 2 100009600 chr9  -      21062894 21062987         74536 Zglp1 
 3 100009600 chr9  -      21063314 21063396         74536 Zglp1 
 4 100009600 chr9  -      21066024 21066377         74536 Zglp1 
 5 100009600 chr9  -      21066940 21067093         74536 Zglp1 
 6 100009600 chr9  -      21062400 21062717         74538 Zglp1

The way that included mouse and human annotations were constructed can be found here.

dipannita-g commented 3 years ago

Hi Shian! Has this been addressed recently? I have a GBK file which I would like to use for importing annotations.

Shians commented 3 years ago

It's very difficult for me to support GTF/GFF/GBK files in general, because of the large range of inconsistencies between annotations from different sources. So for now you will need to create it manually yourself.

I'm actually not too familiar with GBK files, but there's a good chance that rtracklayer::import() will turn it into a half-reasonable table that can be more easily manipulated into the form that NanoMethViz requires.