Signal.UniqueMultiple vs Signal.Unique bedGraphs

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Kohta Ikegami

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Nov 8, 2021, 2:13:13 PM11/8/21
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Hello Alex,

First of all, thanks so much for making this great tool, keeping this up to date, and answering users' every single question!!

Can you clarify how Signal.UniqueMultiple.*.bg and vs Signal.Unique.*.bg files are made and what are the differences between these two files? 

I assume that Signal.UniqueMultiple is from all aligned reads whereas Signal.Unique is only from uniquely-mapped reads? 

Are these files simple base counts of Aligned.sortedByCoord.out.bam, with or without -q 255?

Thanks,

Kohta

Alexander Dobin

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Nov 12, 2021, 6:23:51 PM11/12/21
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Hi Kohta,

you are correct on all points.
The reads-per-base counts by default are normalized to RPM, but you can switch to simple counts with  --outWigNorm None.

Cheers
Alex

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