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williamritchie / IRFinder

Detecting intron retention from RNA-Seq experiments
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The differential IR location information from IRFinder output and ENSEMBLE database doesn't match. #174

Open CYcodeworld opened 1 year ago

CYcodeworld commented 1 year ago

Hi all! First of all thanks for the amazing work on IRFinder. I have identified and classified the differential IR events using IRFinder via GLM based on the criteria "|IR.change|>0.5" and "pvalue<0.05". The next step is to validate these differentially expressed IR events using qPCR. However, when I queried the ensemble database, I found that the chromosomal position information for the ENS IDs recorded in ensemble does not match the position information provided by IRFinder software. For example, for the gene MAMSTR, IRFinder indicates the differential IR position as "MAMSTR/ENSG00000176909.12/clean/chr19:48713550-48713715/-", but according to the ENS ID, its position in the ENSEMBL gene database is "Chromosome 19: 49,215,999-49,222,978". These two intervals do not overlap. How can we explain this discrepancy? eg: 1. the output name information from the Differential IR Analysis output: image

  1. the location information from ensemble (Human (GRCh37.p13)) image I'm excited to use this tool, so any help would be much appreciated!
dg520 commented 1 year ago

@CYcodeworld I believe you were looking at two different versions of references: the Excel one, which I believe is your IRFinder results, refers to GRCh38, while the Ensembl browser one refers to GRCh37.