I am having trouble to find documentation about the circularRNA_known.txt table that circexplorer2 outputs.
Each row gives information about one particular isoform. For example, it can tell you that for a given circRNA, on a given chr, it found x fragments (which I guess refer to the number of reads aligned at the BSJ?), and especially that this correspond to a given isoform that contains exons number x1, x2, etc etc
But how can it know which exons the circRNA contain apart from the exons present at the BSJ?
I use STAR, which finds the chimeric reads and from my understanding, these reads are just giving information about the BSJ.
Any hint on that would be much appreciated, and/or some documentation about the outputs and methods because the manual only describe the commands and briefly the output.
Thank you for your help!
Hello,
I am having trouble to find documentation about the circularRNA_known.txt table that circexplorer2 outputs. Each row gives information about one particular isoform. For example, it can tell you that for a given circRNA, on a given chr, it found x fragments (which I guess refer to the number of reads aligned at the BSJ?), and especially that this correspond to a given isoform that contains exons number x1, x2, etc etc But how can it know which exons the circRNA contain apart from the exons present at the BSJ? I use STAR, which finds the chimeric reads and from my understanding, these reads are just giving information about the BSJ.
Any hint on that would be much appreciated, and/or some documentation about the outputs and methods because the manual only describe the commands and briefly the output. Thank you for your help!