normalized tag count [is] (equal to RPKM reflecting peak density).
But I wonder if this is true: from homer's docs it mentions
Column 6: Normalized Tag Counts - number of tags found at the peak, normalized to 10 million total mapped tags (or defined by the user).
Column 8: Peak score (position adjusted reads from initial peak region - reads per position may be limited)
From looking at the relationship with peak size, I see a clear association between
Normalized Tag Counts vs
Peak Size, but not between
Peak score vs
I have the following questions:
- From the docs, it seems
Column 6: Normalized Tag Countsonly accounts for library size. Is this correct?
Column 8: Peak scorethen account peak size? It is unclear to me what it means "reads per position may be limited"
- Does this mean that
Column 8: Peak scoredoes not account for library size? or should I normalize it in some way to 10m mapped tags?
- Given that I want to look into both wide and narrower peaks equally, which (if any) of the above metrics would you use?
- Which of these metrics could I use as "RPKM"?
Thanks a lot in advance