How to get a gcmodel without the file gc5Base.txt.gz

[scau-drr]

Dear Dr. Wang,

Thank you very much for your excellent software.I have a question that needs your help.

I use the Porcine SNP50 Beadchip from Illumina (50,703 SNP), and now I need gcmodel to adjust the signal. I know that the pig'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 (10 columns) of the latest version of Sus_scrofa 11.1 has not been found on this website. The similar file is only gc5BaseBw.txt.gz (ftp://hgdownload.soe.ucsc.edu/goldenPath/susScr11/database/gc5BaseBw.txt.gz) and the size is only 67 B. I also found the file susScr11.gc5Base.wig.gz (ftp://hgdownload.soe.ucsc.edu/goldenPath/susScr11/bigZips/susScr11.gc5Base.wig.gz) on bigZips, which is very similar to gc5Base.txt.gz, with a size of 9Mb, but with only 9 columns.

I want to know if the file susScr11.gc5Base.wig can be converted to gc5BaseBw.txt? Or can the file susScr11.gc5Base.wig be used to get gcmodel?

Thank you so much! Rongrong Ding.

[kaichop]

UCSC has changed the data format so the ftp://hgdownload.soe.ucsc.edu/goldenPath/susScr11/database/gc5BaseBw.txt.gz file is not the correct file to use now. The wig file is for each 5bp region, and it is not what should be used either. The correct fiel should just be called gc5Base.txt.gz, without the "Bw" or without the "wig" I actually do not know what file they provide. Are you sure that you see a strong genomic wave that you need to do GC adjustment? Typically this is not needed unless the WF is really high.

On Thu, Jul 11, 2019 at 5:45 PM scau-drr notifications@github.com wrote:

Dear Dr. Wang,

Thank you very much for your excellent software.I have a question that needs your help.

I use the Porcine SNP50 Beadchip from Illumina (50,703 SNP), and now I need gcmodel to adjust the signal. I know that the pig'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 (10 columns) of the latest version of Sus_scrofa 11.1 has not been found on this website. The similar file is only gc5BaseBw.txt.gz ( ftp://hgdownload.soe.ucsc.edu/goldenPath/susScr11/database/gc5BaseBw.txt.gz) and the size is only 67 B. I also found the file susScr11.gc5Base.wig.gz ( ftp://hgdownload.soe.ucsc.edu/goldenPath/susScr11/bigZips/susScr11.gc5Base.wig.gz) on bigZips, which is very similar to gc5Base.txt.gz, with a size of 9Mb, but with only 9 columns.

I want to know if the file susScr11.gc5Base.wig can be converted to gc5BaseBw.txt? Or can the file susScr11.gc5Base.wig be used to get gcmodel?

Thank you so much! Rongrong Ding.

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[oshintogla]

I am facing the same problem as I have to generate CNV calls for species Bos. The problem is when I am using the exactly same name file i.e. gc5Base.txt.gz, no information in output gc model file is obtained except the header line. Not sure which file should be downloaded from Ucsc genome browser to make own gcmodel file. Any help will be appreciated.

[lgmgeo]

Have you checked if your gc5Base.txt.gz file is with or without the 'chr' prefix? Because you should have the same prefix in your signalfile.