Dear all,

please apologize if I missed this information, but I have looked throughout
the documentation and vignettes of the IRanges packages and I could not find
this information:

are the coordinates in IRanges objects considered as "0-indexed" or
"1-indexed"?

I.e. when importing the refGene.txt table (or any) from UCSC, we know that
they are 0-indexed, meaning that the first base is not part of the
gene/transcript/object.
If IRanges are 1-index this means we have to subtract 1 from the start
coordinate precedent in the table when creating an IRanges object from them.

Is it correct?
This can be important to clarify, both when considering overlap of features
and in junctions, since it can shift the correct exon boundaries.

Cheers,

Margherita

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