blastn_single_result
Usage
blastn_single_result(
results_table,
bam_file,
which_result,
num_reads = 100,
hit_list = 10,
num_threads = 1,
db_path,
quiet,
accessions_path,
bam_seqs,
out_path,
sample_name,
fasta_dir = NULL
)Arguments
- results_table
A dataframe of the Metascope results
- bam_file
A sorted bam file and index file, loaded with Rsamtools::bamFile
- which_result
Index in results_table for which result to Blast search
- num_reads
Number of reads to blast per result
- hit_list
Number of how many blast results to fetch per read
- num_threads
Number of threads if multithreading
- db_path
Blast database path
- quiet
Logical, whether to print out more informative messages. Default is FALSE.
- accessions_path
Directory where accession files for blast are stored.
- bam_seqs
A list of the sequence IDs from the bam file
- out_path
Path to output results.
- sample_name
Character string, sample name for output files.
- fasta_dir
Path to where fasta files are stored.