problem opening a .gff file

[Noemi Trabanco]

Hello!
My name is Noemí. I have just installed IGV2.3.25 in a Windows computer (using XP professional) and I am trying to visualize some data from a sequencing project. I have opened the genome and the .bam file and also a .gff file with the annotated genes on my reference genotype, but I can not open the .gff file with the annotation of my genotype of interest. My colleagues have already opened it in theis computers, so it does not seem to be a problem of the file.
When I try to load it an error occur. The window sais "Error parsing line at byte position: org.broad.tribble.readers.LineIteratorImpl@15d59c3, for input source "name of my file"

What can it be??

Thanks in advaced,

Noe

[Jim Robinson]

Hi,

The error message indicates a problem parsing the gff file, your colleagues experience nothwithstanding.   Can you reply and attach the file?

Jim

[Noemi Trabanco]

Hello,
I attach the file. I am using a 32 bits computer, and my colleagues have 64 bits, maybe that's the reason. I try with my MAC OS X, with the 32bit version online, and I have the same error.
Thanks for your quick response.

Noemí

[Jim Robinson]

Thanks for the file.   We do not currently support a FASTA section in gff files.  The parser is failing on the first fasta line, the line that starts with >Chr07.   This is an igv bug, we should just ignore the line.   We'll fix it in the next release,  in the meantime you can work around the problem by deleting the fasta section from the file, specifically everything including and after the line that begins with ##FASTA.

Jim

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[Noemi Trabanco]

Hello again,
So you mean that I have to delete the whole part with the nucleotide sequence?? or just the two lines:
##FASTA
>Chr07

Nevertheless I have a similar .gff file which I can open and I do not get that error, but it also includes a fasta section. The difference with the previous one is that this one has no coordenates por the annotation. I attach it also, so you can have a look.
And the one which is not working in my computer, it does work in my colleagues' one...so is it a problem just for 32bits computers?

[Jim Robinson]

Hi,

Its best to delete the whole section, but most the time they will work
anyway. The problem with the file that was failing is it that the line
starting with >Chr07 was mistaken by the parser as a gff record. This
usually won't happen but the presence of the coordinates separated by
tabs on that line fooled it. I've corrected this for the next release.

There is no difference in 32 vs 64 bit computers in this regard,
although IGV version might be relevant.

[Noemi Trabanco]

Hi,

yes,actually I've tried deleting the whole fasta sequence and it opens and ir seems to work properly. Thank you very much for the information.

Regards

2013/11/27 Jim Robinson <jrob...@broadinstitute.org>

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Noe