My goal is to generate the .gcmodel file for a PennCNV script called cal_gc_snp.pl For this task one necessary input file is a "gc5" annotation file which can be downloaded from genome.ucsc.edu
I tried to download the gc file from the Table Browser, but every download has the limitation of 10,000,000 of rows.
The only GC5 file I found is http://hgdownload.cse.ucsc.edu/gbdb/bosTau8/bbi/gc5BaseBw/gc5Base.bw (1,5 GBytes)
However when I tried to view its contents, it is binary encoded. And the "file" command reports: Sendmail frozen configuration - version \260Q\001 so I guess is not valid as input of cal_gc_snp.pl
There is also: http://hgdownload.cse.ucsc.edu/goldenPath/bosTau8/database/gc5BaseBw.txt.gz but is only 66 bytes. And in the same path there is a SQL schema: http://hgdownload.cse.ucsc.edu/goldenPath/bosTau8/database/gc5BaseBw.sql but nothing else (without the annotations).
Any location where I can download the proper gc5 file?
Hello Hope you get your answer till now. Now i have the same questions as yours. Can you please guide about it now?