I am trying to use the sailfish-cir to quantify circular RNAs in my samples. I ran my paired ended RNAseq samples through BWA-mem and subsequently CIRI. Lastly, I parse it through sailfish-cir.
I have a problem trying to interpret the information. In CIRI’s output, it displays information is in terms of coordinates (e.g., 1:805799|810170) but in sailfish-cir, it is different (e.g., ENST00000641515) shown in the quant.sf file. I am not sure whether I have missed a step so that the representation of the gene "name" is different. Could anyone give me some advice?