| run_primer_blastn {rCRUX} | R Documentation |
Runs blastn with the input primer sequences converted to a primer_fasta file as a query
run_primer_blastn(
primer_fasta,
db,
ncbi_bin = NULL,
task = "blastn-short",
word_size = 7,
evalue = "3e+07",
align = "10000000",
coverage = 90,
perID = 50,
reward = 2
)
primer_fasta |
path to the primer fasta file |
db |
a path to a directory / or directories containing one or more blast-formatted database. For multiple blast databases, separate them with a space and add an extra set of quotes. (e.g blast_db_path <- "/my/ncbi_nt/nt" or blast_db_path <- '"/my/ncbi_nt/nt /my/ncbi_ref_euk_rep_genomes/ref_euk_rep_genomes"') |
ncbi_bin |
is the path to blast+ tools if not in the user's path. Specify only if blastn and blastdbcmd are not in your path. The default is ncbi_bin = NULL - if not specified in path do the following: ncbi_bin = "/my/local/ncbi-blast-2.10.1+/bin/". |
task |
the task for blastn to perform - default here is "blastn_short", which is optimized for searches with queries < 50 bp |
word_size |
is the fragment size used for blastn search - smaller word sizes increase sensitivity and time of the search. The default is word_size = 7 |
evalue |
is the number of expected hits with a similar quality score found by chance. The default is evalue = '3e-7'. |
align |
is the maximum number of subject hits to return per query blasted. The default is align = '10000000'. - to few alignments will result in no matching pairs of forward and reverse primers. To many alignments can result in an error due to RAM limitations. |
coverage |
is the minimum percent of the query length recovered in the subject hits. The default is coverage = 90. |
perID |
is the minimum percent identity of the query relative to the subject hits. The default is perID = 50. |
reward |
is the reward for nucleotide match. The default is reward = 2. |
Calls blastn with a primer fasta file as the query. The user can not add additional search parameters, but can modify the available parameters.
run_primer_blastn takes a fasta file containing primers, uses blastn-short to query them to a blast formatted database. The result is an output table with the following columns of data: qseqid (query subject id), sgi (subject gi), saccver (subject accession version), mismatch (number of mismatches between the subject a query), sstart (subject start), send (subject end), staxids (subject taxids).
Information about the blastn parameters can be found by accessing blastn -help and at NCBI.
Note: The number of alignments returned for a given blast search is hardcoded at "-num_alignments 10000000".
a tibble 'output_table' representing the blastn results