How can I get only the 10 best hits from the blast, instead of 500 ? And choose which sequence to blast, from a multifasta file

mhahsler / rBLAST

Interface for the Basic Local Alignment Search Tool (BLAST) - R-Package

GNU General Public License v3.0

105 stars 22 forks source link

Closed cgapp13 closed 2 years ago

cgapp13 commented 2 years ago

Hello,

Thanks for this useful package!

I am trying to blast a multifasta file, and I would like to get only the 10 best hits for each sequence, instead of 500. Is it possible?

Also, can I blast only a selected sequence from my multifasta file? For example, the 3rd sequence out of 50 sequences.

Kind regards,

Chloé

cgapp13 commented 2 years ago

Ok, by searching a little, I find a solution to my first problem, using the BLAST_args = " -max_target_seqs 10" in the predict function!

mhahsler commented 2 years ago

The BLAST arg is the way to go.

About blasting only some sequences: I think the intended way to do that is to just subset the sequences first.

cgapp13 commented 2 years ago

Thank you for your answer, I'll try!