GFF error when converting to binary
francicco opened this issue · 0 comments
francicco commented
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
I don't understand what I'm doing wrong, and how I can fix it.
Thanks a lot
F