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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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blast_nt for nucleotide against NCBI database #15

Closed antoine4ucsd closed 11 months ago

antoine4ucsd commented 11 months ago

Hello thank you for developping this set of tools I am trying to run my nucleotide sequences againts NCBI database From your vignette, it should be blast_n()? but the function is not available is the version of metablastr I just installed with

devtools::install_github("drostlab/metablastr", build_vignettes = TRUE, dependencies = TRUE)

do you have an alternative to this function for nucleotides? https://drostlab.github.io/metablastr/reference/blast_protein_to_nr_database.html

does the database need to be stored locally? advices?

thank you!

HajkD commented 11 months ago

Hi @antoine4ucsd

Happy to hear that metablastr is useful for your research.

Currently, there is no analog to the blast_protein_to_nr_database() function for nucleotides implemented yet, but I can put it on the TODO list.

As for the NR database, yes it would need to be locally stored.

I hope this helps.

Cheers, Hajk

antoine4ucsd commented 11 months ago

thank you. I figured an alternative approach (terminal).

HajkD commented 11 months ago

Just as a comment: the strength (and purpose) of metablastr is not running the search itself (this can be done easily via the terminal), but rather how to process and pipe the BLAST result output back into an R session for downstream analytics with dplyr and other tidy tools.