normalization bam file

[Schelarina]

Hello,
I have 3 smallRNA seq libraries mapped to the genome. I realized they are different in size. How do I normalize the libraries starting from bam files?
thanks

[Brian Bushnell]

Are you sure they need to be the same size? FPKM, for example, is already normalized by read count.

But if you DO want to make them the same size, you can subsample with Reformat to make them all the same size. I suggest subsampling from the original fastq, then mapping, rather than subsampling from a bam file.

[dpryan]

This is generally taken care of when you calculate differential expression. Any program meant to handle this (DESeq2, edgeR, etc.) computes a size factor that's used to correct for this. Have a look at something like miRdeep2 if you're new to looking at small RNAs.