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PolyTailConfig.md

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Custom Poly Tail Configuration

Dorado supports estimation of Poly(A/T) tails for DNA (PCS AND PCB) and RNA samples. The default settings are optimized for non-interrupted Poly(A/T) sequences that occur at read ends.

Dorado also supports additional features that can be customized through a configuration file (described below):

  • Custom primer sequence for cDNA tail estimation
  • Clustering of interrupted Poly(A/T) tails
  • Estimation of Poly(A/T) length in plasmids

Poly(A/T) Reference Diagram

cDNA

5' ---- ADAPTER ---- FRONT_PRIMER ---- cDNA ---- poly(A) ---- RC(REAR_PRIMER) ---- 3'

OR

5' ---- ADAPTER ---- REAR_PRIMER ---- poly(T) ---- RC(cDNA) ---- RC(FRONT_PRIMER) ---- 3'

dRNA

3' ---- ADAPTER ---- poly(A) ---- RNA ---- 5'

Plasmid

5' ---- ADAPTER ---- DNA ---- FRONT_FLANK ---- poly(A) ---- REAR_FLANK --- DNA ---- 3'

OR

5' ---- ADAPTER ---- RC(DNA) ---- RC(REAR_FLANK) ---- poly(T) ---- RC(FRONT_FLANK) ---- RC(DNA) ---- 3'

Configuration Format

The configuration file needs to be in the toml format.

[anchors]
front_primer = "ATCG"
rear_primer = "CGTA"
plasmid_front_flank = "CGATCG"
plasmid_rear_flank = "TGACTGC"

[threshold]
flank_threshold = 0.6

[tail]
tail_interrupt_length = 10

Configuration Options

Option Description
front_primer Front primer sequence for cDNA
rear_primer Rear primer sequence for cDNA
plasmid_front_flank Front flanking sequence of poly(A) in plasmid
plasmid_rear_flank Rear flanking sequence of poly(A) in plasmid
flank_threshold Threshold to use for detection of the flank/primer sequences. Equates to (1 - edit distance / flank_sequence)
primer_window Window of bases at the front and rear of the rear within which to look for primer sequences
tail_interrupt_length Combine tails that are within this distance of each other (default is 0, i.e. don't combine any)