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williamritchie / IRFinder

Detecting intron retention from RNA-Seq experiments
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integration with SIRFindeR #107

Closed ojziff closed 4 years ago

ojziff commented 4 years ago

Hi Dadi and others,

As per the new SIRFindeR tutorial I wondered if adding the equivalent filtering step for low coverage based on exonic & intronic abundances, would make the IRFinder IR ratios more stable e.g. IRratio > 0 & SplicesMax > 100

Many thanks, Oliver

dg520 commented 4 years ago

Hi @ojziff ,

I'm not familiar with S-IRFinderR, the latest IR tool developed by Dr. Ritchie's team, which I was not involved in. In general, increase cutoff for spliceMax in IRFinder will increase the stability of IR ratio measurement while will decrease the total number of IR detected in the sample. Please note, spliceMax in IRFinder is in "the number of reads" unit, meaning it is directly correlated to your RNASeq depth. If your overall sequencing depth is low, a high cutoff at 100 might end up with no IR detected.

Best, Dadi