Using bowtie2 with circle-map

[nguyenkduy0510]

Hi,

Sorry if this was asked before. My library prep was adapted from the Regenberg lab's eccDNA protocol. I tried bowtie2 to align to the reference and then did circle-map realign. I followed the steps from the circle-map realign tutorial (only difference is bowtie2 vs bwa). It gave me the following error message (see attached) and also "cannot convert float NaN to interger" message near the end.