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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.
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