search_from_fastq_reads
identify the matches
from a list of search strings
search_from_fastq_reads(
fastq_file,
search_tables,
skip_n_reads = 0,
progress = TRUE,
max_n_reads = -1,
quality_offset = 33,
output_temp_result = TRUE,
temp_result_folder = "./temp_results",
simplify_id = TRUE,
output_read_length = TRUE,
bp = MulticoreParam()
)
fastq file containing the runs to search from
a dataframe with the following columns: - ["id"],"type",["sequence"],"strand","result","extra","match_ref_seq"
number of reads to skip, default is 0
whether to show the progress bar
maximum number of reads to read, default to -1 (all)
the quality offset to use, default to 33
whether to output the temporary results
directory to output the temporary results
simplify and shorten the read id to the first part
whether to output the read length, NULL - do not output; csv - output to csv file; data - output to result
BiocParallel backend to use for parallelization
will return a list of dataframe containing: - `search_id`, `sequence`, `reads`, `raw_match`, `mean_qualities`, `indexes`.