Using changeseq with Cpf1

[CloeP]

We followed the protocol for CIRCLE-seq using a Cpf1 nuclease (made sure to do end-repair) and then sequenced our samples on a MiSeq V3 600 PE run. This sequencing run produced FASTQ files that appear to contain okay quality data (checked with FASTQC and looked at % reads mapped).

We have successfully installed CHANGE-Seq and it runs on the sample data set. However, we would like some guidance on parameters to change for use with a CPf1 nuclease. When we run the "identify" command we get empty output files, as if there are no cut sites identified in either our control or target samples. No error is produced, the command runs, but doesn't populate the output files. Using IGV with our BAM file we do see read pileup at the expected on-target site and not in the control file, thus we assume we are using the CHANGE-Seq software incorrectly and that is why we aren't getting output.

Any information and help would be greatly appreciated.

[ChristineMarie]

Did you ever solve this issue? I am experiencing the same problem.