FAQ       Help    Low expression levels RNA-seq data filtering Question ID 112 Category Qlucore Omics Explorer   Analysis Date Created 2015-09-21 11:45:40 Date Updated 2015-09-21 11:48:12 How to filter away genes with low expression levels from RNA-seq data? Answer This is applicable to data that has been imported as BAM-files into Qlucore Omics Explorer. The data are represented on the log2(FPKM) scale, incorporating TMM normalization factors in the between-sample normalization step. 1.Set the threshold in the data tab to 0 (will be automatically changed to 1e-6). This will exchange all values below this value to 1e-6. 2. Perform a minimum variance filtration, by moving the variance slider in the statistics dialogue a minimum step to the right. This will remove all genes where all results are the same (e.g. 1e-6). 3. Save a list of the remaining genes. 4. Remove the threshold in order to restore the original values for the remaining genes. 5.Use the list as input in your analysis. (You can save this as a new gedata-file, where you select the option to only save the active variables.) Related articles How to import data (RNA-seq, Illumina, Affymetrix, 10x, Agilent, Wizard, tab separated, csv, txt, bam) Working with RNA-seq data (bam) 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 10X single cell data Normalization of imported RNA-seq data Normalize RNA-seq data in R RNAseq and array technologies RNA-seq normalization for BAM files Was this information helpful?   Back to Search Results