bam2DNAStringSet2

convert bam file to aligned fasta file

Tools for reading and writing biological sequences in multiple
formats, including 'FASTA', 'PHYLIP', 'CLUSTAL', 'STOCKHOLM', 'MEGA' and
'GenBank'. Supports interleaved and sequential layouts where applicable,
and reads or writes gzip, bzip2 and xz compressed files transparently.
Converts between formats, renames sequences via a two-column mapping,
summarizes sequence counts, lengths, GC content and ambiguous characters,
and manipulates sequence sets (e.g., filtering by patterns and computing
consensus sequences from alignments). Also includes functions to download
nucleotide records from NCBI by accession.

Guangchuang Yu

seqmagick

Sequence Manipulation Utilities

bam2DNAStringSet2 function

<dl><dt>bamfile</dt>
<dd>bam file</dd>
<dt>refseq</dt>
<dd>refseq, DNAStringSet object</dd></dl>

Arguments

Author

bam2DNAStringSet2 — bam2DNAStringSet2

<dl>

<dt>bamfile</dt>
<dd>bam file</dd>


<dt>refseq</dt>
<dd>refseq, DNAStringSet object</dd>

</dl>

bam2DNAStringSet2: bam2DNAStringSet2

Description

Usage

Value

Arguments

Author