Query sequence from a FASTA file given a set of ranges, including compound regions like transcripts and junction reads. This assumes the sequence is DNA.
1 2 3
String of bedtools command line arguments, as they would be entered at the shell. There are a few incompatibilities between the docopt parser and the bedtools style. See argument parsing.
Path to a FASTA file, or an XStringSet object.
Path to a BAM/BED/GFF/VCF/etc file, a BED stream, a file object, or
a ranged data structure, such as a GRanges, as the query. Use
Force strandedness. If the feature occupies the antisense strand, the sequence will be reverse complemented.
Given BED12 or BAM input, extract and concatenate the sequences from the blocks (e.g., exons).
As with all commands, there are three interfaces to the
Parses the bedtools command line and compiles it to the equivalent R code.
Accepts R arguments corresponding to the command line arguments and compiles the equivalent R code.
Evaluates the result of
R_bedtools_getfasta. Recommended only for
demonstration and testing. It is best to integrate the compiled
code into an R script, after studying it.
It is recommended to retrieve reference sequence using a
BSgenome package, either custom or provided by
getSeq to query for
specific regions of the BSgenome object. If one must access a file,
consider converting it to 2bit or FA (razip) format for indexed
import and its
But if one must access a FASTA file, we need to read all of it with
readDNAStringSet and extract regions using
gr is a GRanges or GRangesList.
A language object containing the compiled R code, evaluating to a DNAStringSet object.
getSeq, the primary sequence query interface.
1 2 3 4 5 6 7 8
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.