The Reason of Offset Handling for Negative Strand Coordinates

[yangzhao1230]

There is an offset added when handling negative strand coordinates:

if strand == "-":
    offset = 1
    strand_ = "minus"
else:
    offset = 0
    strand_ = "plus"

From my understanding, the coordinates on the positive and negative strands should be equivalent, with the only difference being the orientation. In other projects, like BEND, they simply reverse complement the sequence without adding an offset for the negative strand.

My background in biology is limited, so I would greatly appreciate any insights or explanations on this matter. Understanding the rationale behind this implementation would help in ensuring the accurate use of genomic data in my analysis.

[junhong-huang]

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[jzthree]

This is due to how the transcription start site is annotated in our files. Offset is needed to make sure that the transcription start site is at the same position in the sequence no matter whether it is on "+" or "-" strand.

[junhong-huang]

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