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drostlab / metablastr

Seamless Integration of BLAST Sequence Searches in R
https://drostlab.github.io/metablastr/
GNU General Public License v2.0
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Reg: Reciprocal hits from already run blast outcomes #9

Closed harish0201 closed 2 years ago

harish0201 commented 3 years ago

Hi!

I have performed the following to obtain blast format 6 tabular format:

  1. A vs B with Diamond
  2. B vs A with Diamond

I read AvB.hits and BvA.hits using read_blast() function. Will it be possible to identify the reciprocal hits? Or should I rerun the searches with metablastr?

HajkD commented 3 years ago

Hi Harish

Many thanks for contacting me.

Could you please provide me a small example script?

Are you using rdiamond or metablastr or both?

This will help me to help you better.

Cheers, Hajk

harish0201 commented 3 years ago

Hi!

These were run directly via diamond. At this stage, I was not using rdiamond or metablastr.

So basically, I ran diamond to obtain hits in the tabular (6) format, which is the default diamond output, and reading them via read_blast() function under metablastr.

HajkD commented 3 years ago

Hi,

Do you want to try read_diamond() in my R package rdiamond?

Cheers, Hajk

HajkD commented 3 years ago

Passing an existing BLAST/DIAMOND output into the blast_reciprocal_best_hit() function is currently not possible and I can see this as a feature request.

harish0201 commented 3 years ago

Hi!

Sorry, I didn't get any notifications from GitHub. I'll play around with rdiamond!