[maker-devel] jbrowse not working

[Emmanuel Nnadi]

Hi Carson
Thanks for the reply

I generated the off with this command gff3_merge –d
dpp_contig.maker.output/dpp_contig_master_datastore_index.log

I had to rerun browse with the following command

maker2jbrowse
/Users/emmannaemeka/desktop/Gpm/maker/data/mucuna/muc1_genome_snap2.maker.output/muc1_genome_snap2.functional_blast.gff\maker2jbrowse
-d
/Users/emmannaemeka/Desktop/Gpm/maker/data/mucuna/muc1_genome_snap2.maker.output/muc1_genome_snap2_master_datastore_index.log
\-out /Library/WebServer/Documents/JBrowse-1.12.1/muc/muc_jb


Although its showing


WARNING: No matching features found for mRNA I don't know what it means


I don't understand what it means


Successfully, I was able to setup the jbrowse local host. I had to move the
jbrowse folder to my local host


The jbrowse is up and running however, I have about 18488 contigs only 31
contigs are showing, how can i make all my contigs to show on jbrowse?




Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
Publications:
https://www.researchgate.net/profile/Emmanuel_Nnadi/publications

On Tue, Oct 10, 2017 at 1:35 AM, Carson Holt <carsonhh at gmail.com> wrote:

> Is muc1_genome_snap2.all.gff missing embedded fasta entries at the end of
> the file? That can happen if you use the -n option with gff3_merge.
> Alternatively it’s possible one of the individual contig gff3 used to build
> the merged gff3 is truncated. If that is the case then gff3_merge should
> have thrown some sort of error or warning when you run it.
>
> Thanks,
> Carson
>
>
>
>
> On Oct 7, 2017, at 3:34 PM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
>
> Please,
> I ran the command line
>
> maker2jbrowse muc1_genome_snap2.all.gff
>
> The command created some folders. However, at the end it read
> No reference sequences defined in configuration, nothing to do.
>
> Please what does it mean? How can I view it in jbrowse.
>
> Thanks
>
>
> Nnadi Nnaemeka Emmanuel
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/
> publications
>
>
>
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