Question: Normalizing Human Samples in .bam format
0
gravatar for mittu1602
10 weeks ago by
mittu160250
mittu160250 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 10 weeks ago by Devon Ryan73k • written 10 weeks ago by mittu160250
0
gravatar for Devon Ryan
10 weeks ago by
Devon Ryan73k
Freiburg, Germany
Devon Ryan73k 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 10 weeks ago by Devon Ryan73k

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 10 weeks ago by mittu160250

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

ADD REPLYlink written 10 weeks ago by Devon Ryan73k
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