Dear Apollo Email List Members,
I am a new member to this email list.
My name is Sandra Loevenich and I am graduate student.
I am writing to you in order to hopefully get help on Apollo.
I have mass spectrometry based peptide sequences from D. melanogaster
that are currently not anticipated by the FlyBase annotation.
I did a tblastn of the peptides and now have the chromosomal
coordinates.
I have been able to create valid FlyBase-ChadoXML files using a
FlyBase bulk download script.
I also have installed the latest version of Apollo and the Flybase-
ChadoXML files can be loaded in Apollo. That is all fine.
The problem comes in when I create my own gff files with aiming to
display my peptides in Apollo.
A combination of chadoXML that works and a gff that does *not* work
for Apollo and Apollo's STDOUT/STDERR
file is here: http://www.biocompute.de/apollo-gff-problem.tgz
I used an online GFF3-validator (wormbase) and that says that the GFF3
file is valid. However, Apollo does not parse it.
Maybe you can see where the problem is?
Thank you very much!!!
Sincerely,
Sandra Loevenich
Sandra Loevenich
ETH Zurich, IMSB, HPT D71
Wolfgang-Pauli-Str. 16
8093 Zurich, Switzerland
phone: +41 44 633 30 47
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