search

GMOD / jbrowse

JBrowse 1, a full-featured genome browser built with JavaScript and HTML5. For JBrowse 2, see https://github.com/GMOD/jbrowse-components.
http://jbrowse.org
Other
460 stars 199 forks source link

Tabix error #1629

Closed francicco closed 2 years ago

francicco commented 2 years ago

Hi,

I'm trying to convert a gff3 file in its binary for to use it under jbrowse/apollo. The plain text file gff3 file I'm using it's like this

RPCZ01000001.1  annotation  gene    164112  168197  .   +   .   ID=Thar.Scf0000969G1;Name=Thar.Scf0000969G1
RPCZ01000001.1  annotation  mRNA    164112  168197  60  +   .   ID=Thar.Scf0000969G1.1;Parent=Thar.Scf0000969G1
RPCZ01000001.1  annotation  exon    164112  164159  60  +   .   ID=exon1_Thar.Scf0000969G1.1;Parent=Thar.Scf0000969G1.1
RPCZ01000001.1  annotation  start_codon 164112  164114  60  +   .   ID=exon1_Thar.Scf0000969G1.1;Parent=Thar.Scf0000969G1.1
RPCZ01000001.1  annotation  CDS 164112  164159  60  +   0   ID=cds_of_Thar.Scf0000969G1.1;Parent=Thar.Scf0000969G1.1
RPCZ01000001.1  annotation  exon    166214  166523  60  +   .   ID=exon2_Thar.Scf0000969G1.1;Parent=Thar.Scf0000969G1.1
RPCZ01000001.1  annotation  CDS 166214  166523  60  +   0   ID=cds_of_Thar.Scf0000969G1.1;Parent=Thar.Scf0000969G1.1
RPCZ01000001.1  annotation  exon    167467  167584  60  +   .   ID=exon3_Thar.Scf0000969G1.1;Parent=Thar.Scf0000969G1.1
RPCZ01000001.1  annotation  CDS 167467  167584  60  +   2   ID=cds_of_Thar.Scf0000969G1.1;Parent=Thar.Scf0000969G1.1
RPCZ01000001.1  annotation  exon    167764  167871  60  +   .   ID=exon4_Thar.Scf0000969G1.1;Parent=Thar.Scf0000969G1.1
RPCZ01000001.1  annotation  CDS 167764  167871  60  +   1   ID=cds_of_Thar.Scf0000969G1.1;Parent=Thar.Scf0000969G1.1
RPCZ01000001.1  annotation  exon    168087  168197  60  +   .   ID=exon5_Thar.Scf0000969G1.1;Parent=Thar.Scf0000969G1.1
RPCZ01000001.1  annotation  CDS 168087  168194  60  +   1   ID=cds_of_Thar.Scf0000969G1.1;Parent=Thar.Scf0000969G1.1
RPCZ01000001.1  annotation  stop_codon  168195  168197  60  +   .   ID=exon5_Thar.Scf0000969G1.1;Parent=Thar.Scf0000969G1.1

I sort it and compress it like this:

bgzip Test.gff && tabix -p gff Test.gff.gz

When I load it under Jbrowse the compressed gff returns me an error, while the same file in plain text looks just fine

Screenshot 2022-03-25 at 18 41 00

I don't understand what I'm doing wrong, and how I can fix it. Thanks a lot F

cmdcolin commented 2 years ago

I think it is telling you the feature with ID exon5_Thar.Scf0000969G1.1 appears twice with different types. While technically allowed for features to have the same ID, they should not have different types. I'd make them have different IDs for clarity

francicco commented 2 years ago

Hi, @cmdcolin, If I remove start and stop codon doesn't change anything F

cmdcolin commented 2 years ago

If it still gives errors mentioning start codon after you've removed start codon, you may need to clear your browser cache perhaps or make sure you are using the new file?

francicco commented 2 years ago

Cache problem That worked thanks!

F

cmdcolin commented 2 years ago

Super :)