Has anyone seen a wierd junctions file as an output. Although most of my paired-end reads aligned to the genome (both pairs), my junctions.bed file doesn't link together many of my exons. In fact, most of the links that were made are not even between exons, rather they were intergeneic and scattered.
This is not due to loading it onto the wrong assembly. Has anyone else had this problem with paired end reads?
This is not due to loading it onto the wrong assembly. Has anyone else had this problem with paired end reads?
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