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Picard::CollectRnaSeqMetrics Expecticed/Minimum Values for Sample QC

I'm using CollectRnaSeqMetrics from the Picard toolbox but I'm having trouble finding expected/minimum for the metrics. I would like to apply these metrics to QC RNAseq samples. There are some obvious issues (e.g. high rRNA%) but for other metrics it is less clear what is: concerning, problematic, acceptable...

Q1) Can I use these metrics to identify problematic/concerning samples?

Q2) Where can I find examples of good/okay/bad values for each of these metrics?

Thank you, Ben

Edit: We are using rRNA exclusion prep.

rna-seq qc picard collectrnaseqmetrics
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written by bkellman • bkellman

1 answer

Broadly speaking, it depends on your library and sequencing strategy. For example:

  • 3'->5' bias: If you are using an oligo(dT) strategy, then you may get overrepresentation of 3' ends. See http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3821180/ as an example
  • Intron/exon content: Again, polyA+ libraries tend to have higher exon content, whereas ribo-depleted or other strategies may have more intronic content.

A few more useful papers:

• 2 views • link
written by fanli.gcb fanli.gcb

Thanks, I'll check out the links. We used rRNA depletion for prep.

• 2 views • link
written by bkellman • bkellman

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