FAQ       Help    How does Qlucore calculate the length of the gene to do the normalization? Question ID 102 Category Qlucore Omics Explorer   Analysis Date Created 2015-03-19 09:48:51 Date Updated 2022-01-07 08:19:19 How does Qlucore calculate the length of the gene to do the normalization, i.e., after receiving BAM files and BEFORE TMM? A gene, such as p53, may have many isoforms which have different exons. So how does Qlucore calculate the gene length in order to do the normalization? Taking the longest, the shortest or the union of the exons or something else? Answer Qlucore computes the gene lengths from the union of all isoforms for the gene. We use the “entire exon length” of each gene.Overlapping exons are collapsed to a disjoint union of intervals. Related articles Normalization of RNAseq data in Qlucore Omics Explorer Agilent arrays BAM file sort order Biosulfite sequencing ChIP-seq and ATAC-seq Data pre-processing for expression data Gene lengths for count data How are counts counted when importing bam files? How is the normalization (mean=0, Var=1) done in Omics Explorer? How to import data (RNA-seq, Illumina, Affymetrix, 10x, Agilent, Wizard, tab separated, csv, txt, bam) Low expression levels RNA-seq data filtering Normalization of imported RNA-seq data Normalization using housekeeping genes Normalization Z-score (mean=0, var=1) calculations Normalizing PCR (QPCR or Q-PCR) data Quantile normalization and eliminated factors RNA-seq normalization for BAM files TPM values for RNASeq Working with RNA-seq data (bam) Was this information helpful?   Back to Search Results