Question: Normalizing Human Samples in .bam format
0
gravatar for mittu1602
8 months ago by
mittu1602140
India
mittu1602140 wrote:

Hello All,

On going through some R packages like DeSeq2 for normalizing data I couldn’t get a normalized output. I would like to know if there is any other alternate way to normalize these human samples which are from Illumnia sequencing platform, paired-end data and in .bam format.

Thank you

ADD COMMENTlink modified 8 months ago by Devon Ryan79k • written 8 months ago by mittu1602140
0
gravatar for Devon Ryan
8 months ago by
Devon Ryan79k
Freiburg, Germany
Devon Ryan79k wrote:

If "normalized output" is meant to mean "normalized counts", then in DESeq2 it's counts(dds, normalized=TRUE). If you're looking for something else then you need to clarify exactly what you want.

ADD COMMENTlink written 8 months ago by Devon Ryan79k

I have 4 control samples and to run an analysis I need these 4 controls as "one single sample" which needs to be normalized.

ADD REPLYlink written 8 months ago by mittu1602140

Average the normalized counts then (presuming whatever you're doing accepts that).

ADD REPLYlink written 8 months ago by Devon Ryan79k
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