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!
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!
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