|RNA-seq normalization for BAM files|
|Is FPKM (or RPKM) calculated when BAM files are imported?|
|That is an option that can be selected during the import. Other options are TPM and TMM.|
Differences between FPKM and TMM: The TMM based expression values calculated by Qlucore OE for RNA-seq data are similar to log2(RPKM). The difference is that Qlucore OE normalizes the counts not only by the total number of counts in the different samples, but also incorporates a sample-specific normalization factor with the aim of accounting for differences in RNA composition between samples. The normalization factor is calculated by the "TMM" approach by Robinson and Oshlack (2010). It has been shown (e.g., by Dillies et al (2012)) that this type of normalization performs better than normalizing only with respect to the total number of counts (as is done with RPKM).
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