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adoebley / Griffin

A flexible framework for nucleosome profiling of cell-free DNA
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chrX and chrY in GC mappability pipeline #15

Closed savarsinha123 closed 1 year ago

savarsinha123 commented 1 year ago

Hello,

I had a question about the GC mappability pipeline. When I looked through the scripts, it seems as though the GC bias is only calculated for chromosomes 1-22. Is there a way to also configure the GC mappability pipeline to work with the X and Y chromosomes as well, or does the pipeline only work with autosomes.

Thanks! Savar Sinha

adoebley commented 1 year ago

Hi, Thank you for the question and sorry for the huge delay in responding. The GC bias is calculated for the whole sample and doesn't vary by chromosome. The X and Y are ignored when calculating GC bias because they aren't (always) present in 2 copies and this difference in coverage would change the GC bias if they were included.

savarsinha123 commented 1 year ago

Ah I see, thank you for your response!