Re: [Gmod-ajax] fasta setup

[Scott C. <sc...@sc...>]

Hello Zhihao,

There are a few things I would check:

* Did the browser reload/refresh really work? With javascript and json
files, browsers can be very conservative about caching.  There are a few
ways to get around this: open the browser's dev tools and turn off caching
explicitly, or open the URL in a incognito/private window.
* In the data/seq directory, do you see entries in the refSeqs.json file
for both chromosomes?
* Also in the data/seq directory, do you see two directories, one for each
chromosome?

Scott


On Fri, May 3, 2019 at 8:10 AM Zhihao Ding <zhi...@gm...> wrote:

> Dear Jbrowse developers,
>
> Thanks for developing Jbrowse. I've been trying to setup an instance
> following the instructions. I am able to see the browser page, but haven't
> managed to get the reference sequence right.
>
> I've downloaded a couple of fasta files just for testing from the
> following link
> ftp://ftp.ensembl.org/pub/release-96/fasta/homo_sapiens/dna/
>
> I then run the following two commands:
> bin/prepare-refseqs.pl --fasta
> Homo_sapiens.GRCh38.dna_rm.chromosome.1.fa.gz
> bin/prepare-refseqs.pl --fasta
> Homo_sapiens.GRCh38.dna_rm.chromosome.2.fa.gz
>
> This is  trackList.json generated:
> {
>    "formatVersion" : 1,
>    "tracks" : [
>       {
>          "category" : "Reference sequence",
>          "chunkSize" : 20000,
>          "key" : "Reference sequence",
>          "label" : "DNA",
>          "seqType" : "dna",
>          "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
>          "type" : "SequenceTrack",
>          "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
>       }
>    ]
> }
>
> On the browser page, I have only contig 1 in the dropdown list.
>
> Could anyone point me to the right directions here?
>
> Thank you,
> Zhihao
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research