0 or 1-based coordinates

[KSLiu98]

Hi SUPPA2 community:

I’m using SUPPA for the first time, and I’m impressed with the ease of use. I do have a question, however, about the coordinates used to identify local events. It isn’t immediately clear to me whether the coordinates used are 0 or 1 based. I was wondering if I could get some clarification on this. Thanks!

--Kevin.

[EduEyras]

Hi, thanks for the message The coordinates are 1-based. Each number corresponds to the actual position in the chromosome where that annotation (eg. start or end of an exon) is located. All numbers in SUPPA refer to starts or ends of an exonic region (see Fig. 3 in the github) https://github.com/comprna/SUPPA?tab=readme-ov-file#generation-of-transcript-events-and-local-alternative-splicing-events 0-based coordinates are specific of the BED and other formats built from it (https://genome.ucsc.edu/FAQ/FAQformat.html) I hope this helps Eduardo

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On Thu, 8 May 2025 at 07:11, KSLiu98 ***@***.***> wrote: *KSLiu98* created an issue (comprna/SUPPA#212) <#212> Hi SUPPA2 community: I’m using SUPPA for the first time, and I’m impressed with the ease of use. I do have a question, however, about the coordinates used to identify local events. It isn’t immediately clear to me whether the coordinates used are 0 or 1 based. I was wondering if I could get some clarification on this. Thanks! --Kevin. — Reply to this email directly, view it on GitHub <#212>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADCZKB34EMCV24AORAYKADL25JZJVAVCNFSM6AAAAAB4U4ZOWSVHI2DSMVQWIX3LMV43ASLTON2WKOZTGA2DOMJXHE4TMOA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>