FAQ       Help    Gene lengths for count data Question ID 135 Category Qlucore Omics Explorer   Data Import Date Created 2019-12-17 15:37:08 Date Updated 2024-11-22 13:06:56 For count data, how do I normally get access to gene lengths? Answer The Wizard can be used to import count data if data is not delivered as bam files. Normalization methods such as TMM requires the length of all included genes. The gene length are a normal output from count generation software tools such as Salmon and HTSeq. The Gene length can be set and changed from the data tab. For single cell data gene lengths should be 1 (depending on the technique, but true for 10x genomics and many other). This is because only the tail of each gene is kept and the number of reads is thus not proportional to the length of the gene. Related articles DESeq2 Normalization of RNAseq data in Qlucore Omics Explorer Analyze data from Array Express Analyzing Flow Cytometry data Convert from R to Qlucore data file format How do I know how much I should filter by variance or by statistical tests such as ANOVA How does Qlucore calculate the length of the gene to do the normalization? How to import 10X single cell data How to import data (RNA-seq, Illumina, Affymetrix, 10x, Agilent, Wizard, tab separated, csv, txt, bam) How To Import TCGA Data Import Affymetrix data Import annotations Loading and creating annotations Manual import of data and annotations from GEO Normalization of imported RNA-seq data Save RNA-seq or Affymetrix files as .gedata Two colored arrays Use .sra files Was this information helpful?   Back to Search Results