Confusion about GC and RT correction

[CHENAO-QIAN]

Hi,

When processing WES with ASCAT, I saw both the reference files of GC and RT correction files available for downloading, and the scripts to generate my own GC and RT correction files. I am wondering

1. Can I can download these files and apply to my data directly, or is it better that I generate these files for my own data? What is the difference?
2. The QC results gave me GC_correction_after 500bp=0/100kb=0; RT_correction_after Gm12812=0. Is this expected?

Thank you!

[tlesluyes]

Hi @CHENAO-QIAN,

1. If you use our pre-generated loci and allele files, I suggest you also use our matched pre-generated RT/GC correction files. The scripts mostly help people with custom designs (microarrays or targeted-seq) deriving their own set of correction files.
2. Yes, it is expected. Before the correction (GC_correction_before & RT_correction_before), values are likely not 0 so the logR needs to be corrected for such covariates. Then, after the correction (GC_correction_after & RT_correction_after), one should expect correlations to be 0 since ASCAT corrected the logR track.

Cheers,

Tom.

[CHENAO-QIAN]

Thank you for the explanation, Tom!