Hi, I have a problem trying to understand/interpret the results of the sailfish-cir. I went through the manual and article a few times, but I still don't fully grasp the interpretation of it.
Supposedly I saw a putative back splice junction (BSJ) coordinate produced by CIRI (circular RNA identifier by Gao et al (2015)) - chr17:43057051|43115779 - corresponding to BRCA1. Sailfish-cir will generate a TPM value for the said coordinate as well. And from my understanding of the article (and the developer), the value is actually a proportion of circRNA and linear transcripts. However, sailfish-cir also produces TPM values pertaining to the transcript IDs of BRCA1. I.e., There is a fair chance that all of the transcript IDs related to BRCA1 would should a TPM value.
So my question are:
1) How should I go about interpreting the information? Should I see TPMs that are related to BRCA1 or only for the BSJ's? 2) Is the TPM for BSJ only for BSJ? 3) Is the TPM for transcript IDs only for respective transcript? 4) If I want to know how does the expression of circRNA (i.e., the BSJ's) is presenting, how should I go about analyzing it? 5) Supposedly points 2 & 3 are true, is the ratio of circRNA suppose to be calculated as (BSJ) / (BSJ + transcript ID)?
Hope someone can help clarify these confusion. Thank you.
