get_seqs: Gets sequences from bam file
In compbiomed/MetaScope: Tools and functions for preprocessing 16S and metagenomic sequencing microbiome data
View source: R/metascope_blast.R
get_seqs R Documentation
Gets sequences from bam file
Description
Returns fasta sequences from a bam file with a given taxonomy ID
Usage
get_seqs(id, bam_file, n = 10, bam_seqs)
Arguments
id
Taxonomy ID of genome to get sequences from
bam_file
A sorted bam file and index file, loaded with
Rsamtools::bamFile
n
Number of sequences to retrieve
bam_seqs
A list of the sequence IDs from the bam file
Value
Biostrings format sequences
compbiomed/MetaScope documentation built on Sept. 23, 2024, 5:25 a.m.
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View source: R/metascope_blast.R
| get_seqs | R Documentation |
Gets sequences from bam file
Description
Returns fasta sequences from a bam file with a given taxonomy ID
Usage
get_seqs(id, bam_file, n = 10, bam_seqs)
Arguments
id |
Taxonomy ID of genome to get sequences from |
bam_file |
A sorted bam file and index file, loaded with Rsamtools::bamFile |
n |
Number of sequences to retrieve |
bam_seqs |
A list of the sequence IDs from the bam file |
Value
Biostrings format sequences
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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