Generating custom error profile

[stacy-l]

Hello,

I'm interested in using Sim-it to simulate PacBio Revio HiFi CCS system reads. I know that the profile may not be significantly different from the Sequel II HiFi CCS error profile, but I'd still like to be careful about my simulations if possible :)

I cannot find the custom script to generate error profiles – would it be okay for you to share that, either to the repo or by email?

Best,
SL

[ndierckx]

Hi, Sorry for the late response, I added the script to the repo.
To run it you need to use this command: perl train_error_profile.pl -ref reference.fasta -reads ONT_or_PacBio.fasta
Don't use the reference of a complete genome, that would take too long... Do you have a reference sequence and reads that align to it?

[stacy-l]

Hi, also sorry for the late response! Thanks a ton for adding the script.

I don't have locus-specific aligned reads, but I could generate that fairly quickly. If I have trouble running the script, I'll post again :)