I tried finding information on CIRI's output details, but there is little to go around. Could someone help me with the interpretation?
1) So in the column heading, CIRI's output has the '#junction_reads', does this mean that there were X amount of junctions found within the start & end coordinates, or does it mean there are X amount of reads that fall within a junction or is this actually represented by the #non_junction_reads?
2) May I also know what does SM_MS_SMS means? I couldn't find anything online. Usually it is presented in this format - e.g., 2_2_0, 13_11_0, 8_8_1, etc.
3) Is the junction_reads_ratio a "confidence" indicator, to tell the user that the junctions are more probable than coincidence? Because this is only one interpretation as to the initial assumption in point 1.
4) Am I right to say that the circRNA type or geneID are only stated when a circRNA annotation is featured with the option '--anno'? But does CIRI just read the coordinates and apply the details? Would de novo construction of junctions be limited when annotation files are added?
5) I completely don't understand what does the 'junction_reads_ID' mean. Could I get some idea how to interpret it please?
Any information would be useful. Thank you very much for your time.