Normalizing Human Samples in .bam format

Question

[mittu1602]

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

Answer 1

[Devon Ryan]

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.

[mittu1602]

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

[Devon Ryan]

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