circexplorer2 output

Question

[npont]

Hi all!

I am desperately searching for information about the output of circexplorer2, namely "circularRNA_known". I do not find any explanation about the columns exonCount and fragment for example.

Could someone provide resources or, better, explain a bit more the following:

• Do the "exonCount" correspond to the number of exons in the circRNA? --> If no, what does it correspond to? --> If yes, how can we know this number while, from my understanding, the tool solely get the number of exons that our reads overlap at the BSJ (and which btw depend on the read length of our paired-end reads)?
• Do "fragment" correspond to the number of reads that map the circRNA?

I find an incoherence, because if you look at the screen that I join here 1 : it states that we have 2 exons, respectively of size 78 bp and 120 bp but they both start at position 157.

Thank you for your help, very much appreciated.

[GenoMax]

This link in manual is describing the file in question and the columns: https://circexplorer2.readthedocs.io/en/2.3.8/modules/annotate/#output

The particular column you are describing is not in the list (this is the latest version of documentation). Are you perhaps running an older version?

[npont]

You are right, I was not naming the columns correctly. The "exonStarts" is named exonOffset. However, even if we have description of the name of the columns of circularRNA_known on the link you shared it is not clear how they map paired-end reads to get information about the exon content of the circRNA.

Would you have understood if the 1st mate is the one mapped to the junction and the 2nd mate is the one giving information about the exon content inside the circRNA? Or both mates are mapped at the junction? It seems like the circexplorer2 always consider exons that are consecutive (example: exons 14,15,16,17 no alternative splicing inside the circRNA) and give a number of exons that cannot be overlapped by my reads length. I have mates of each 150bp but it detects sometimes a number of exons with length superior to 2*150

Thank you for any help, I would very much appreciate :)