Dear sir,
I am using the bovine SNP770k Beadchip from Illumina , and now I need gcmodel to adjust the signal.
I know that the cow's gcmodel can be obtained with the script cal_gc_snp.pl and requires a special file gcfile.
Gcfile can be downloaded from the UCSC website, but the file gc5Base.txt.gz (14 columns) of the latest version of BosTau9 has not been found on this website. The alomost similar file is only gc5BaseBw.txt.gz (ftp://hgdownload.soe.ucsc.edu/goldenPath/BosTau9/database/gc5BaseBw.txt.gz) and the size is only 66 B.
I also found the file Bostau8.gc5Base.wig.gz (ftp://hgdownload.soe.ucsc.edu/goldenPath/BosTau8/bigZips/BosTau8.gc5Base.wig.gz) on bigZips, which is very similar to gc5Base.txt.gz, with a size of 1.5GB, but with only 13 columns.
Dear sir, I am using the bovine SNP770k Beadchip from Illumina , and now I need gcmodel to adjust the signal. I know that the cow's gcmodel can be obtained with the script cal_gc_snp.pl and requires a special file gcfile. Gcfile can be downloaded from the UCSC website, but the file gc5Base.txt.gz (14 columns) of the latest version of BosTau9 has not been found on this website. The alomost similar file is only gc5BaseBw.txt.gz (ftp://hgdownload.soe.ucsc.edu/goldenPath/BosTau9/database/gc5BaseBw.txt.gz) and the size is only 66 B. I also found the file Bostau8.gc5Base.wig.gz (ftp://hgdownload.soe.ucsc.edu/goldenPath/BosTau8/bigZips/BosTau8.gc5Base.wig.gz) on bigZips, which is very similar to gc5Base.txt.gz, with a size of 1.5GB, but with only 13 columns.
what file will be used for my analysis, Sir.
Thank you so much!