get_multi_seqs: Gets multiple sequences from different accessions in a bam...

In compbiomed/MetaScope: Tools and functions for preprocessing 16S and metagenomic sequencing microbiome data

Gets multiple sequences from different accessions in a bam file

Description

Returns fasta sequences from a bam file with given taxonomy IDs

Usage

get_multi_seqs(ids_n, bam_file, seq_info_df, metascope_id_tax, sorted_bam_file)

Arguments

ids_n	List of vectors with Taxonomy IDs and the number of sequences to get from each
bam_file	A sorted bam file and index file, loaded with Rsamtools::bamFile
seq_info_df	Dataframe of sequence information from metascope_blast()
metascope_id_tax	Data.frame of taxonomy information
sorted_bam_file	Filepath to sorted bam file

Value

Biostrings format sequences

compbiomed/MetaScope documentation built on Nov. 5, 2024, 9:25 p.m.