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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...