Hi,

I am aware that for any RNAseq based downstream analysis, many uninformative reads need to be filtered, for example, low quality reads, unmapped reads, non-unique reads etc. This is based on literauture survey.

How important are singleton reads (from a paired end reads RNAseq experiement) for an allele specific expression analysis, where reads on a particular allele is counted based on a variant calling file. Should they be considered?