Hi Binu,
It is possible that the BLAT format has changed and broken the adapter.
I could take a look at the file if you forward the BLAT results
along with the GBK and GFF3 files.
Did you convert the BLAT output to GFF or GFF3 format? The GFF
format supported in Apollo is one used by the Ensembl folks, so it
might not work with data generated elsewhere. You really want to
use the GFF3 format. If it is in GFF3 format, I could take a
look at the generated file and see what might have gone wrong.
Cheers,
Ed
On Tue, 9 Feb 2010, Binu George wrote:
Hi,
I am new to using the Apollo genome browser, and am having some trouble
trying to overlap BLAT result output with my sequence information.
We have genbank and gff file containing the genomic sequence of a contig
from a genome. I am able to use apollo to view this data along with all
the annotations.
Along with that, we have the result of a BLAT run of mRNA sequences matched
against this genbank file (in .psl format). We are trying to overlay the
BLAT result over the currently view contig data, but are unable to do so.
On trying to open the '.psl' file, we get this error logged in the
'stdout.log'
file
-----------
ERROR: Failed to parse blat data
-----------
We converted the .psl to gff format. But on trying to load this gff file
doesn't work either. The popped up dialog box freezes, and there is no
corresponding message logged in the stdout/stderr log files.
Any help in this regard is appreciated!
Thanks!
--Binu
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