Annotations using GS Mpper

[pmishra1982]

I am using GS mapper for mapping reads to reference. I was wondering whether some one has already done the annotation of the reads using GS Mapper. I usually use our in-house wrapper annotation tool to do this.

The manual says that "-fd" OR "-annot" option can be used to annotate the reads/run while running GS Mpper. But I always get an error while using these options.

Is the mapper looking for a specific format?

Thanks.

[nickloman]

Is the mapper looking for a specific format?

Think it wants GoldenPath format, IIRC.

[pmishra1982]

Thanks for the reply.
But the manual says that it looks for refGene.txt file. Is there a free software to convert GFF file to the GoldenPath file format ( I guess its called AGP file).

[kmcarr]

The refGene.txt file format refers to the file which corresponds to the UCSC Table Browser refGene table. Here is a link to the table schema description: http://genome.ucsc.edu/cgi-bin/hgTab...e+table+schema

I don't know of any scripts available to convert a GFF file to this table format.

[pmishra1982]

@kmcarr:Thanks for the format.
I looked into the UCSC browser description but this is mostly for Human genomes. I am working on Ricketssia. Generally I use our in-house wrapper to give me annotations which outputs in the standard Genbank format. So to get the exons and other information, I have to run it through something like GENSCAN? Has any body worked on bacteria to extract annotations directly from the 454 data using GS Mapper?