how to override the option "--ignore 06.fixstart.contigs_to_not_change" when running circlator all

[yjx1217]

Hello,

I have a circlator run for which I want to reset the start point using my own starting gene. When I just run with circlator fixstart, it worked as expected. However, when I run with circlator all, the start point was not reset. I noticed a file named 06.fixstart.contigs_to_not_change was generated this time and the contig matching with my specified starting gene is in this file. And according to this manual (https://github.com/sanger-pathogens/circlator/wiki/Task:-all), the option "--ignore 06.fixstart.contigs_to_not_change" is automatically activated by default, which should be responsible for my problem. I was wondering if there is a way to directly disable the option "--ignore 06.fixstart.contigs_to_not_change" when running circlator all? Or have I to run an extra step of circlator fixstart to get around?

Thanks in advance!

Best, Jia-Xing

[martinghunt]

When you run circlator all, it tries to circularize all the contigs. The names of the ones that could not be circularized are written to the file 06.fixstart.contigs_to_not_change. When fixstart is run at the end, contigs in that file are not changed, because they were not recognised as circular, and so it doesn't make sense to change the start position.

[yjx1217]

Hi Martin,

Thanks for the explanation! It makes sense. I got several PacBio contigs (assembled by canu) from a single circular genome (yeast mitochondrial genome). Even with circlator, I still cannot assemble them back to a single contig. I will try different settings based on the manual on trouble shooting (https://github.com/sanger-pathogens/circlator/wiki/Troubleshooting). Please let me know if you have some recommended parameters for my use case. Thanks!

Best, Jia-Xing