Focus on quality control & “filtering” in RNAseq analysis

It is tempting to filter the data to get “good counts”

• low quality alignments
• PCR duplicates

But..

• Why low quality reads should be skipped if they were aligned ? Is the implicit hypothesis "low quality read are miss-mapped" a likely hypothesis ?

• When we remove PCR duplicates (exact same sequence and exact same location), are we sure that we remove PCR duplicates ? What are the metrics that support the implicit hypothesis that read with same sequence & same location are PCR duplicates ?

Reflect of miRNA sequencing...