isoform annotation

[CKoernerDKFZ]

Hello,

we have been working with the TCGA isoform.quantification files for a while until we realized that it seems like the chromosomal end position annotated in that file does not match the actual chromosomal end position of the read. At least we experienced dramatic dicrepancies between the TCGA dataset and all other datasets we have looked at which can be only explained by an offset of 1 in the annotation of the chromosomal end position. Would you have any idea how this can be the case? Or any alternative explanations for the discrepancy we are observing?

Thank you very much for your help,

Cindy

[rbowlby1]

Hi Cindy,

You are correct. The end coordinate in the isoform.quantification.txt file is exclusive (offset by 1). In the near future we will update the Github pipeline code to make this end coordinate inclusive. Thank you for your message, and we apologize for the inconvenience.