FAQ       Help    RNA-seq normalization for BAM files Question ID 81 Category Qlucore Omics Explorer   Analysis Date Created 2013-11-28 10:20:47 Date Updated 2017-09-11 12:45:47 Is FPKM (or RPKM) calculated when BAM files are imported? Answer 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). Related articles BAM file sort order Biosulfite sequencing ChIP-seq and ATAC-seq How are counts counted when importing bam files? How does Qlucore calculate the length of the gene to do the normalization? How to import data (RNA-seq, Illumina, Affymetrix, 10x, Agilent, Wizard, tab separated, csv, txt, bam) Low expression levels RNA-seq data filtering Working with RNA-seq data (bam) Was this information helpful?   Back to Search Results