TideHunter Racon compatibility?

Hello,

I was wondering if you planned on implementing racon within the tool? Or maybe an output that racon can take?

Thanks, Chang

Dec 09 '19 10:12 cnk113

Hi, Thanks for your interest in TideHunter! I think very likely that Racon will improve the quality of the consensus produced by TideHunter.

Dec 09 '19 12:12 yangao07

I don't have any plan recently since I have been occupied with some other projects. Do you have any suggestions about that? Thanks!

Dec 09 '19 12:12 yangao07

Sorry I got sidetracked, but I was planning on using MarginPolish + HELEN to improve the accuracy. I was thinking of using the first consensus of the POA (as it is currently), and then use the subreads by realigning to the consensus and pass that into MarginPolish. Does that make sense?

Jan 03 '20 09:01 cnk113

So I guess would it be possible for Tidehunter to output all the subreads as well?

Jan 03 '20 18:01 cnk113

I see your point and I think it makes sense.

Jan 05 '20 12:01 yangao07

I will try to add additional output for the subreads information so that you can implement your idea. Will update a release when it is done.

Jan 05 '20 12:01 yangao07

In the latest release (https://github.com/yangao07/TideHunter/releases), the subread position information is now output as a ',' separated string in the output file. Please try it and let me know if it works for you! Yan

Jan 09 '20 11:01 yangao07

Thanks, I'll try this over the weekend.

Jan 09 '20 19:01 cnk113

Just found a bug in v1.2.0, please not try it until I fixed it. Sorry about that. Will get back to you later.

Jan 15 '20 01:01 yangao07

Please try the latest version, v1.2.1 (https://github.com/yangao07/TideHunter/releases). Bugs are fixed now.

Jan 16 '20 07:01 yangao07

Check out the -u/--unit-seq option in the latest release: v1.4.0. It will give you all the unit sequences of each tandem repeat.

May 19 '20 08:05 yangao07