Deeptools bamcoverage Scaling factor & EdgeR/DE-Seq nromaliztion factors

[Jaritz,Markus]

Dear colleagues,

first, thank you for this wonderful tool!

I recently came across some ATAC-Seq samples that needed normalization, and I used EdgeR (and DE-Seq) to derive the associated normalization factors.

The derived factors are for example 1.3 for one sample, which means that counts should be >downscaled< for this sample as the library size will be multiplied by this factor (counts/(lib.size*1.3)).

Am I correct that such normalization factors (x) have to be passed on as "1/x" , rather than "x", to the "--scaleFactor" argument (in addition to --normalizeTo1x or --normalizeUsingRPKM) ? In the example case, this would be 1/1.3 (~0.77).

In other words, do I understand correctly that the --scaleFactor arguments will, at the end, simply multiply the coverage by the passed on scaleFactor? Then the sample will be >upscaled< in bamCoverage, as counts are multiplied by 1.3. And this is not what I want.

Sorry if this is a trivial question, and thank you for your time.

Kind regards

Markus

Dr. Markus Jaritz
Busslinger - Bioinformatics
IMP - Research Institute of Molecular Pathology
Dr. Bohr-Gasse 7
1030 Vienna
Austria

Tel: +43 1 79730 - 3780
Fax: +43 1 797 30 223780
email: jar...@imp.ac.at

[Friederike Dündar]

Hi Markus,

the number indicated via --scaleFactor will be used to multiply the raw read count.

You can see the respective line of code here (line 351):
https://github.com/fidelram/deepTools/blob/master/deeptools/writeBedGraph.py

return args['scaleFactor'] * tile_coverage[0]

ATAC-seq was raised as a topic at least once here in the mailing list, if you wanted, you could search for the entry and get in touch with the person who used deepTools for ATAC-seq to exchange more expertise (ideally via the mailing list, so that everyone can benefit - alternatively, we'd be happy to add a section about ATAC-seq to our documentation if you wanted to share your insights in how deepTools can help there)

Best,

Friederike

--
You received this message because you are subscribed to the Google Groups "deepTools" group.
To unsubscribe from this group and stop receiving emails from it, send an email to deeptools+...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.