Strandedness Downstream Analysis

[jfear]

What does it do?

• Develops strandedness downstream analysis
• Creates final classification for strandedness

Definition of done

• [x] Plots depicting patterns of strandedness throughout SRA.

  See notebook/deliver/strandedness_downstream_analysis for distribution plot.

• [x] Table classifying each SRR.

  See output/strandedness_downstream_analysis.pkl for dataframe with values and flags.

• first_strand is the value of PicardRNASeqMetrics when aligned in first strand mode.

• second_strand is the value of PicardRNASeqMetrics when aligned in second strand mode.

• indicator_strand is an indicator variable of strandedness

  • 0 == unstranded
  • 1 == moderate first stranded
  • 2 == well first stranded
  • -1 == moderate second stranded
  • -2 == well second stranded

• num_srr is the number of SRRs for an SRX

• flag_strand_identical_among_srr is a flag where True if strandedness was the same across all SRRs within an SRX.

  • This only looks for direction not magnitude (i.e., 1 and 2 are treated as the same, but 1 and 0 or 1 and -1 are different).