Hi! I am really enjoying using CIRIquant for my BSJ quantification. However, I am currently analyzing samples which I expect to have a low number of circRNA (no RNase R treatment). However, when I look at the output GTFs for all samples, all circRNAs have a BSJ count of 1.000. While I expect them to be lowly abundant, this seems highly unlikely to me (because I am still detecting 1000's of unique BSJs). I also find quite some circRNAs that overlap between samples, having in each sample on 1.000 BSJ count. Would you have any explanation for this? Thanks!
Hi! I am really enjoying using CIRIquant for my BSJ quantification. However, I am currently analyzing samples which I expect to have a low number of circRNA (no RNase R treatment). However, when I look at the output GTFs for all samples, all circRNAs have a BSJ count of 1.000. While I expect them to be lowly abundant, this seems highly unlikely to me (because I am still detecting 1000's of unique BSJs). I also find quite some circRNAs that overlap between samples, having in each sample on 1.000 BSJ count. Would you have any explanation for this? Thanks!