FAQ       Help    How are counts counted when importing bam files? Question ID 101 Category Qlucore Omics Explorer Date Created 2015-03-19 09:41:44 Date Updated 2015-03-19 09:48:31 How are counts counted when importing bam files? For instance, the HTSeq-count offers different modules (see http://www-huber.embl.de/users/anders/HTSeq/doc/count.html#usage) Answer The count mode Omics Explorer uses corresponds exactly to "intersection_strict" in HTSeq-count. All modes (union, intersection_strict etc) have certain advantages depending on the level of trust you have in the annotation of your data. If you are confident that the data is correctly annotated, and you want to avoid counting DNA reads (as opposed to RNA reads) or reads from genes that are not correctly spliced (i.e. genes with remaining introns) the intersection_strict mode is a good choice. Using union mode on the other hand allows for a greater amount of uncertainty in the model. Related articles BAM file sort order Biosulfite sequencing ChIP-seq and ATAC-seq 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 RNA-seq normalization for BAM files Working with RNA-seq data (bam) Was this information helpful?   Back to Search Results