singleton reads RNAseq downstream analysis

Question

[prasundutta87]

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?

Answer 1

[Devon Ryan]

If the singleton is still informative then keep it. You're throwing a lot of data out when doing allele-specific stuff, don't make life harder than needed.

[prasundutta87]

Thank you for the reply. The singletoms are mapping and hence I kept them.