seqsToAln

cigar

The set of sequences corresponding to the cigars, as Biostrings::DNAStrings

dnaseq

The target region to return, as GRanges.  Sequences overlapping
the target region are trimmed to exactly match it.

target

The character to represent deleted bases. Default "-"

del_char

Genomic start locations of aligned sequences. Should be
used in conjunction with target_start and target_end.

aln_start


Creates a one-to-one text alignment of a set of cigar strings with respect
to the reference sequence by collapsing insertions and introducing gaps
across deletions.<p></p><p>When genomic coordinates for the alignment start and the target region
are provided, aligned sequences are cropped to the target region
</p>

CrispRVariants provides tools for analysing the results of a
CRISPR-Cas9 mutagenesis sequencing experiment, or other sequencing experiments
where variants within a given region are of interest. These tools allow users to
localize variant allele combinations with respect to any genomic location (e.g.
the Cas9 cut site), plot allele combinations and calculate mutation rates with
flexible filtering of unrelated variants.

Helen Lindsay

CrispRVariants

Tools for counting and visualising mutations in a target location

seqsToAln function


Creates a one-to-one text alignment of a set of cigar strings with respect
to the reference sequence by collapsing insertions and introducing gaps
across deletions.

When genomic coordinates for the alignment start and the target region
are provided, aligned sequences are cropped to the target region


seqsToAln: Creates a text alignment from a set of cigar strings

Description

Usage

Arguments

Value