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[SimonChen1997]

Hi! I would like to ask about the meaning of "feature distance", "Similar guide distances", and "target_seq30" in the csv report.

[mjfos2r]

Hi, I'm not sure if this is being actively maintained given the major shifts happening across many US federal agencies, but I'll answer your questions.

Feature distance

This is an integer representing the number of nucleotides from the guide to the associated feature; measured from the nearest edge of the guide to the start of the feature. This is used to filter guides based on the parameters you've set for --before and --into.
You can find more details by looking at the class method: guidemaker.core.Annotation._filter_features()

Similar guide distances

This is the edit distance of a guide to its nearest neighbors.

• hamming or levenshtein set by --dtype
  This is used to filter out highly similar guides depending on the values set for --dist which represents the minimum edit distance from any other potential guide.

given a simple set of guides:

- g1: "ACGT-AC-G-TA-A"
- g2: "ACGT-AC-G-TA-G"
- g3: "ACGT-AC-C-TA-G"
- g4: "TTTT-TT-T-TT-T"

The distances are:

• G1 <-> G1: 0
• G1 <-> G2: 1
• G1 <-> G3: 2
• G1 <-> G4: 8

target_seq30

This a 30bp sequence centered around the guide that is used in Doench efficiency scoring.

It is the sequence corresponding to 27bp upstream from the end of the PAM, and 3bp downstream from the end of the PAM.

For both PAM orientation:
3prime: 5'-[7bp][guide][PAM][3bp]-3'
5prime: 5'-[3bp][PAM][guide][7bp]-3'