[Gmod-gbrowse] Sequence not appear on gbrowse_details

[Irwandwiyanto]

I tried running gbrowse2 accordance with the installation instructions ,
gbrowse2 already working on localhost and graph databases have also appeared
, but when trying to view details gene DNA sequence does not appear , is
there any thing wrong in the installation ??



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[Alexey Morozov]

You mean DNA sequence as in ACTGTACA... thingie? Gbrowse doesn't display it
directly: you should either view object properties (default function for
click, as I recall) or use sequence download addons,

Post by Irwandwiyanto
I tried running gbrowse2 accordance with the installation instructions ,
gbrowse2 already working on localhost and graph databases have also appeared
, but when trying to view details gene DNA sequence does not appear , is
there any thing wrong in the installation ??
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[Irwandwiyanto]

I tried to create a new data but still does not appear on gbrowse_details
<Loading Image...>



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[Alexey Morozov]

I'm not sure I get the question. The sequence shows okay for yeast, but
your genome DB doesn't open correctly? Or is there something wrong with how
gbrowse_details displays yeast sequence?
If it's your genome, please send Gbrowse.conf and your DB's conf file.

Post by Irwandwiyanto
I tried to create a new data but still does not appear on gbrowse_details
<
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[Irwandwiyanto]

this is link GBrowse.conf and databases
http://goo.gl/QRZZTd



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[Alexey Morozov]

That's weird; configs seem alright to me. What file format do you store
your sequences in? If it's GFF3, don't forget to include separate
definition lines for scaffolds or contigs. Example:

scaffold00001 newbler contig 1 1348726 . . .
ID=scaffold00001;Name=scaffold00001
.....other stuff....
scaffold00001 maker gene 56082 56739 . + . ID=4447-gene;Name=4447-gene
scaffold00001 maker mRNA 56082 56739 . + .
ID=4447;Parent=4447-gene;Name=4447;_AED=0.02;_eAED=0.02;_QI=0|0|0|1|1|1|2|0|184
scaffold00001 maker exon 56082 56220 . + . ID=4447:exon:0;Parent=4447
scaffold00001 maker exon 56324 56739 . + . ID=4447:exon:1;Parent=4447
scaffold00001 maker CDS 56082 56220 . + 0 ID=4447:cds;Parent=4447
scaffold00001 maker CDS 56324 56739 . + 2 ID=4447:cds;Parent=4447
scaffold00001 maker gene 63275 63728 . + . ID=4448-gene;Name=4448-gene
scaffold00001 maker mRNA 63275 63728 . + .
ID=4448;Parent=4448-gene;Name=4448;_AED=0.02;_eAED=0.03;_QI=0|0|0|1|1|1|2|0|97;Note=mitochondrial
import inner membrane translocase subunit
tim9-like;Ontology_term=GO:0016020,GO:0046872,GO:0005739,GO:0015031
.......other stuff......

scaffold00001

ACGTACAAACTGAAG....

The first line is the key. If you don't include it, the fasta sequences in
the end (or in the separate file) don't get parsed.

this is link GBrowse.conf and databases
http://goo.gl/QRZZTd
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[Irwandwiyanto]

this my databases
##gff-version 3
##sequence-region chrLG2 1 66492657

chrLG2 GlimmerHMM contig 1 66492657 . + . ID=chrLG2;Name=chrLG2
chrLG2 GlimmerHMM mRNA 47748452 47748949 . + .
ID=p5_sc00005.V1.gene1000;Name=Os02g0307900
chrLG2 GlimmerHMM CDS 47748452 47748949 . + .
ID=p5_sc00005.cds1000.1;Parent=p5_sc00005.V1.gene1000;Name=Os02g0307900;Note=single-exon
chrLG2 GlimmerHMM mRNA 42116662 42123008 . + .
ID=p5_sc00005.V1.gene100;Name=uncharacterized protein LOC100836088
chrLG2 GlimmerHMM CDS 42116662 42118543 . + .
ID=p5_sc00005.cds100.1;Parent=p5_sc00005.V1.gene100;Name=uncharacterized
protein LOC100836088;Note=initial-exon

chrLG2

CCCTAAAcCCTAAACCCTAAACCCTAAACACGAAATCCAAAATCCTAACCCCAAAGTCCTAAACCCTAAG
CCTTAAATTATATACCCTAAATTCaAAATCATAAGCCCTAAACCCTAAGCCCTAAAcCCTAAATCTTAAA

I try to follow what you suggest but the result is still the same
<Loading Image...>



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[Irwandwiyanto]

Dear Mr Alexey Morozov
i try installing gbrowse again with ubuntu 15.04, after installing any
error

Forbidden

You don't have permission to access /cgi-bin/gb2/gbrowse/yeast on this
server.
Apache/2.4.7 (Ubuntu) Server at 10.88.25.48 Port 80

do you help me?

best regards
Duwi Irwanto

2015-01-28 16:38 GMT+07:00 Irwandwiyanto [via Generic Model Organism System

Post by Irwandwiyanto
this my databases
##gff-version 3
##sequence-region chrLG2 1 66492657
chrLG2 GlimmerHMM contig 1 66492657 . + . ID=chrLG2;Name=chrLG2
chrLG2 GlimmerHMM mRNA 47748452 47748949 . + .
ID=p5_sc00005.V1.gene1000;Name=Os02g0307900
chrLG2 GlimmerHMM CDS 47748452 47748949 . + .
ID=p5_sc00005.cds1000.1;Parent=p5_sc00005.V1.gene1000;Name=Os02g0307900;Note=single-exon
chrLG2 GlimmerHMM mRNA 42116662 42123008 . + .
ID=p5_sc00005.V1.gene100;Name=uncharacterized protein LOC100836088
chrLG2 GlimmerHMM CDS 42116662 42118543 . + .
ID=p5_sc00005.cds100.1;Parent=p5_sc00005.V1.gene100;Name=uncharacterized
protein LOC100836088;Note=initial-exon

Post by Irwandwiyanto
chrLG2

CCCTAAAcCCTAAACCCTAAACCCTAAACACGAAATCCAAAATCCTAACCCCAAAGTCCTAAACCCTAAG
CCTTAAATTATATACCCTAAATTCaAAATCATAAGCCCTAAACCCTAAGCCCTAAAcCCTAAATCTTAAA
I try to follow what you suggest but the result is still the same
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