Issue extracting information from refFlat of livestock species

[zihhuafang]

Dear all,

I am wondering if anyone has encountered this issue when using locuszoom in species other than human.

I am working with cattle which has 29 autosomes and have created my own database for it. I also modified the chr2chrom and chrom2chr fuction in locuszoom r script to allow plot correctly for 29 autosomes. Codes:

chrom2chr <- function (x) { y <- substring(x,first=4); as.numeric(y); }

chr2chrom <- function (x) { return (paste("chr",as.numeric(x),sep="")); }

Still, I can only get the correct information from refFlat up to chr22. For the rest of the autosomes, it did not work. When I checked the temporary files, my refFlatRaw and refFlat_in_the_region were empty. However, arg[[chr]] was correct. I have checked that my database does contain information for all the chromosomes.

Does anyone know where else in the script that I need to modify to make it work?

I appreciate any input.

Best wishes, Zih-Hua