<p>This doesn't use R, but a simple and quite convenient method is to use <code>bedtools getfasta</code> with your fasta file. You'll need to make a BED file out of the RepeatMasker output:</p>

<pre><code>awk 'BEGIN{OFS="\t"}{name=sprintf("%s_%s", $10, $11); strand="+"; if($9 == "C"){strand="-"}; print $5,$6-1,$7,name,".", strand}' repeatmasker.output &gt; rmsk.bed
</code></pre>

<p>Then, given that and your <code>genome.fa</code> fasta:</p>

<pre><code>bedtools getfasta -name -s -fi genome.fa -bed rmsk.bed -fo output.fa
</code></pre>

<p>This will produce a multiline fasta file names like <code>AluSx_SINE/Alu</code> (due to the <code>-name</code> option) where the sequences are reverse complemented if appropriate.</p>

<p>You can install bedtools either via conda (<code>conda install -c bioconda bedtools</code>) or <a href="https://github.com/arq5x/bedtools2/releases/download/v2.26.0/bedtools-2.26.0.tar.gz" rel="nofollow noreferrer">github</a>.</p>

CC BY-SA 3.0
2017-12-02T18:07:03.620Z
2017-12-02T18:07:03.620Z
Devon Ryan
<p>I have a very, very long list of genome coordinates of areas. I need to gather a sequence in order to compare it to another database of sequences that I have. How do I produce the genome sequences from these coordinates in R?</p>

<p>I am very new to this and need a detailed answer.</p>

CC BY-SA 3.0
2017-12-01T22:06:32.047Z
What genome? Namely, is it one for which there's already a [BSgenome](http://bioconductor.org/packages/release/BiocViews.html#___AnnotationData) package?
Devon Ryan
CC BY-SA 3.0
2017-12-01T22:36:17.593Z
The genome was given to me, it is not on there. My problem, more specifically I suppose, is that I was given a couple files. The genome was run through RepeatMasker to obtain coordinates of transposable elements. So, I have the coordinates from the map file that was produced from RepeatMasker and I would like to identify the sequences of these coordinates from my genome (which is too big to view). After I obtain the sequences, I will need to compare those sequences to a library of known elements that was also given to me in another file. So, I am lost especially since I am very new to this
Noob
CC BY-SA 3.0
2017-12-01T22:39:18.383Z
OK, does this really have to be done in R? This particular task is a bit better done on the command line than in R.
Devon Ryan
CC BY-SA 3.0
2017-12-27T03:30:28.450Z
Do you know what type of commands this would consist of?
Noob
<r><genome><phylogenetics><ngs>
Coordinates to Genome R Studio Script?
# Coordinates to Genome R Studio Script?

(Asked by: username_0 on 2017-12-01)

I have a very, very long list of genome coordinates of areas. I need to gather a sequence in order to compare it to another database of sequences that I have. How do I produce the genome sequences from these coordinates in R?

I am very new to this and need a detailed answer.

**Tags:** r, genome, phylogenetics, ngs
> **Comments:**
> **username_1**: What genome? Namely, is it one for which there's already a [BSgenome](http://bioconductor.org/packages/release/BiocViews.html#___AnnotationData) package?  
> **username_0**: The genome was given to me, it is not on there. My problem, more specifically I suppose, is that I was given a couple files. The genome was run through RepeatMasker to obtain coordinates of transposable elements. So, I have the coordinates from the map file that was produced from RepeatMasker and I would like to identify the sequences of these coordinates from my genome (which is too big to view). After I obtain the sequences, I will need to compare those sequences to a library of known elements that was also given to me in another file. So, I am lost especially since I am very new to this  
> **username_1**: OK, does this really have to be done in R? This particular task is a bit better done on the command line than in R.  
> **username_0**: Do you know what type of commands this would consist of?  

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## 1 answers

### Answer by username_1 on 2017-12-02. Score: 2

This doesn't use R, but a simple and quite convenient method is to use bedtools getfasta with your fasta file. You'll need to make a BED file out of the RepeatMasker output:
awk 'BEGIN{OFS="\t"}{name=sprintf("%s_%s", $10, $11); strand="+"; if($9 == "C"){strand="-"}; print $5,$6-1,$7,name,".", strand}' repeatmasker.output > rmsk.bed

Then, given that and your genome.fa fasta:
bedtools getfasta -name -s -fi genome.fa -bed rmsk.bed -fo output.fa

This will produce a multiline fasta file names like AluSx_SINE/Alu (due to the -name option) where the sequences are reverse complemented if appropriate.
You can install bedtools either via conda (conda install -c bioconda bedtools) or github.


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