As instructed by the readthedocs I ran CIRI-long collapse following the call command but I'm getting unexpected results.
I have inspected the isoforms generated by CIRI-long call in IGV after aligning them back to my reference genome (which in this case is a plasmid) and they match what I expect. However, collapse generates output like the following:
In some cases corrected clusters will make it through but the number is much lower than the initial set.
Any possible reasons why all circular read clusters are being filtered? I have verified there is no clipping > 20 and the circRNAs are < 200,000 bp (I think these are filters from inspecting the code). I also modified collapse.py to not filter cluster size <= 1 and got the same results.
Hi,
As instructed by the readthedocs I ran CIRI-long collapse following the call command but I'm getting unexpected results.
I have inspected the isoforms generated by CIRI-long call in IGV after aligning them back to my reference genome (which in this case is a plasmid) and they match what I expect. However, collapse generates output like the following:
In some cases corrected clusters will make it through but the number is much lower than the initial set.
Any possible reasons why all circular read clusters are being filtered? I have verified there is no clipping > 20 and the circRNAs are < 200,000 bp (I think these are filters from inspecting the code). I also modified collapse.py to not filter cluster size <= 1 and got the same results.