Input files for Roche GSMapper

[cow_girl]

I am using GSMapper to assemble 454 reads to a reference bovine genome.
I would like to specify a reference genome annotation and so that my variations can be easily identified as occurring in coding regions or not.
I have been over and over the documentation and done alot of searching but I just can't work out what format and directory structure to put my reference genome in!
In the manual it says "the format of this file must match that of the GoldenPath 'refGene.txt' file" but then it doesn't go into any detail.
I understand that this refGene.txt is something that can be downloaded from UCSC but I am working with the bovine genome, so my reference genome will be from NCBI in genbank format.
I would also like to input known SNPs and that's a whole other problem, but would be quite simple I think if I knew how to do the reference genome.
If someone could please give me an idiot's guide to the format and directory structure that my input files need to be in that would be much appreciated.
Thanks!

[flxlex]

It is not that hard to set up, presuming you have Bos taurus as genome:

Set up the following folders
goldenpath (or whatever name suits you)
goldenpath/bt4.0
goldenpath/bt4.0/chromosomes
goldenpath/bt4.0/database

In the chromosome folder, add the ('untarred') chromosome sequences from

http://hgdownload.cse.ucsc.edu/goldenPath/bosTau4/chromosomes/

In the database folder, add the ('untarred') refGene.txt file from

http://hgdownload.cse.ucsc.edu/goldenPath/bosTau4/database/

Set the GOLDENPATH environment variable to this folder, e.g. (in the bash shell):

export GOLDENPATH=/your/folders/goldenPath/

Map reads using:
runMapping bt4.0 reads.sff

Check the 454HCDiffs.txt and 454AllDiffs.txt, they should show the annotation of any variants in the lines starting with '>'.

It's magic!

There does not seem to be a snp file for cow at UCSC, but you could make a file similar to the human one located here:

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/snp130.txt.gz

Good luck!

[cow_girl]

That worked perfectly, thank you! Now just to get my SNP file correct

[Estefania]

Dear All
I have problems using galdenPath with gs mapper (v 2.5.3)
Could anybody help me to find the correct file for human mitochondria? Is it possible to build the file by myself? Have you ever done?
Thanks in advance
Estefania

[sarahrg]

I want to do the same but with human genome... can I specify a file just for the gene I'm using?