[ENHANCEMENT] diff_to_TSS calculated based on genomic coordinates

[ancofer3]

Is there an existing issue for this?

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Have you loaded the SQANTI3.env conda environment?

• I have loaded the SQANTI3.env conda environment

Are you running SQANTI3 on its latest release?

• I have SQANTI3 updated to the latest release

Problem description

When looking at the output in the classification files, in many cases, the diff_to_TSS is larger than the transcript itself. I think this is because the difference is calculated using genomic coordinates. If there is an intron between the TSS and the 5'-end of the read, this difference can be "inflated" and not represent accurately "how far" the read falls from the reference transcript. Maybe, this could be corrected substracting from diff_to_TSS the length of the introns that are between the TSS and the 5' end.

Code sample

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Error

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Anything else?

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