Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-12-06T20:04:50.557Z
Answers.LastActivityDate: 2020-12-06T20:04:50.557Z
Answers.UserDisplayName: Maximilian Press
Body: <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>
  
Tags: <rna-seq><phylogenetics><rna-alignment><bowtie2>
Title: What is the best way to map/align my reads on a given genome?
ThreadText: # 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
  
  
  ---
  
  ## 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.
  
  
  ---
  
  