<p>This is a pretty straightforward analysis, assuming that you want to measure something like &quot;how many reads align to genome 1, and how many reads align to genome 2?&quot;.</p>
<ul>
<li>The <a href="http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#getting-started-with-bowtie-2-lambda-phage-example" rel="nofollow noreferrer">bowtie2 manual has a section</a> on this.</li>
<li>There are <a href="https://wikis.utexas.edu/display/bioiteam/Mapping+with+bowtie2+Tutorial" rel="nofollow noreferrer">other tutorials for bowtie2</a>.</li>
<li><a href="http://bio-bwa.sourceforge.net/" rel="nofollow noreferrer">bwa</a> is also <a href="http://evomics.org/wp-content/uploads/2019/01/genomics_tutorial_2019.pdf" rel="nofollow noreferrer">well-suited to this task</a>.</li>
</ul>
<p>You should be able to then use <a href="http://www.htslib.org/" rel="nofollow noreferrer">samtools</a> to compute <a href="http://www.htslib.org/doc/samtools-stats.html" rel="nofollow noreferrer">statistics</a> on your alignments.</p>

CC BY-SA 4.0
2020-12-06T20:04:50.557Z
2020-12-06T20:04:50.557Z
Maximilian Press
<p>I am frequently using a ballgown package for my rnaseq analysis, but recently I have had a new task to have my reads mapped on two different genomes to understand the level of alignment between the two, therefore I wonder what is the best tool to do this? I have single-end reads.
What I need is to have a percentage of uniquely mapped fragments, mapped to multiple loci and, say, unmapped. Can <code>bowtie</code> do the job? Is there a standard explanation procedure explained elsewhere? Thanks.</p>

<rna-seq><phylogenetics><rna-alignment><bowtie2>
What is the best way to map/align my reads on a given genome?
# What is the best way to map/align my reads on a given genome?

(Asked by: username_0 on 2020-12-02)

I am frequently using a ballgown package for my rnaseq analysis, but recently I have had a new task to have my reads mapped on two different genomes to understand the level of alignment between the two, therefore I wonder what is the best tool to do this? I have single-end reads.
What I need is to have a percentage of uniquely mapped fragments, mapped to multiple loci and, say, unmapped. Can `bowtie` do the job? Is there a standard explanation procedure explained elsewhere? Thanks.

**Tags:** rna-seq, phylogenetics, rna-alignment, bowtie2

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## 1 answers

### Answer by username_1 on 2020-12-06. Score: 1 | Accepted answer

This is a pretty straightforward analysis, assuming that you want to measure something like "how many reads align to genome 1, and how many reads align to genome 2?".

* The [bowtie2 manual has a section](http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#getting-started-with-bowtie-2-lambda-phage-example) on this.
* There are [other tutorials for bowtie2](https://wikis.utexas.edu/display/bioiteam/Mapping+with+bowtie2+Tutorial).
* [bwa](http://bio-bwa.sourceforge.net/) is also [well-suited to this task](http://evomics.org/wp-content/uploads/2019/01/genomics_tutorial_2019.pdf).

You should be able to then use [samtools](http://www.htslib.org/) to compute [statistics](http://www.htslib.org/doc/samtools-stats.html) on your alignments.


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