Answers.Body: <p>The seeds are clustered together by proximity to a selected set of ‘anchor’ seeds in the 2nd phase of the STAR algorithm,  but this •clustering/stitching/scoring process• is not present in Bowtie2.</p>
  <p><a href="https://i.sstatic.net/izJSN.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/izJSN.png" alt="enter image description here" /></a></p>
  <p><a href="https://drive.google.com/file/d/1l8dAS9fA3wpPiExRXGIJ4aE4gJltl_1A/view?usp=sharing" rel="nofollow noreferrer">mapping by performing a two-step process</a></p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-08-14T04:02:29.477Z
Answers.LastActivityDate: 2022-08-14T04:02:29.477Z
Answers.UserDisplayName: envs_h_gang_5
Answers.Body: <blockquote>
  <p>What is the fundamental difference between STAR and Bowtie(2).</p>
  </blockquote>
  <p>STAR for mapping spliced (i.e. with introns) short RNA-seq reads against a genome. Bowtie2 for mapping short reads without splicing.</p>
  <blockquote>
  <p>Would my downstream analysis be incorrect if I use Bowtie2 where STAR was supposed to be used (?)</p>
  </blockquote>
  <p>Yes. If you use bowtie2 to map spliced short reads against a genome, STAR-based downstream analysis is likely to be wrong.</p>
  <blockquote>
  <p>... and vice versa?</p>
  </blockquote>
  <p>If you map genomic reads with STAR, the result will be suboptimal. Use the right tool for the right task.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-08-14T04:48:09.160Z
Answers.LastActivityDate: 2022-08-14T04:48:09.160Z
Answers.UserDisplayName: user172818
Body: <p>What is the fundamental difference between STAR and Bowtie(2). Specifically, what is the difference in their final output (regardless of run-time differences, speed, memory usage etc.). Both seem to work on the same kind of input *.fastq files without discriminating what they are associated with and generate an output version of the *.fastq files. Would my downstream analysis be incorrect if I use Bowtie2 where STAR was supposed to be used, and vice versa? Thank you.</p>
  
Tags: <phylogenetics><bowtie2><star>
Title: STAR vs Bowtie2
ThreadText: # STAR vs Bowtie2
  
  (Asked by: username_0 on 2022-08-14)
  
  What is the fundamental difference between STAR and Bowtie(2). Specifically, what is the difference in their final output (regardless of run-time differences, speed, memory usage etc.). Both seem to work on the same kind of input \*.fastq files without discriminating what they are associated with and generate an output version of the \*.fastq files. Would my downstream analysis be incorrect if I use Bowtie2 where STAR was supposed to be used, and vice versa? Thank you.
  
  **Tags:** phylogenetics, bowtie2, star
  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_2 on 2022-08-14. Score: 6
  
  > What is the fundamental difference between STAR and Bowtie(2).
  
  STAR for mapping spliced (i.e. with introns) short RNA-seq reads against a genome. Bowtie2 for mapping short reads without splicing.
  
  > Would my downstream analysis be incorrect if I use Bowtie2 where STAR was supposed to be used (?)
  
  Yes. If you use bowtie2 to map spliced short reads against a genome, STAR-based downstream analysis is likely to be wrong.
  
  > ... and vice versa?
  
  If you map genomic reads with STAR, the result will be suboptimal. Use the right tool for the right task.
  
  
  ---
  
  ### Answer by username_1 on 2022-08-14. Score: 4
  
  The seeds are clustered together by proximity to a selected set of ‘anchor’ seeds in the 2nd phase of the STAR algorithm, but this •clustering/stitching/scoring process• is not present in Bowtie2.
  
  [![enter image description here](https://i.sstatic.net/izJSN.png)](https://i.sstatic.net/izJSN.png)
  
  [mapping by performing a two-step process](https://drive.google.com/file/d/1l8dAS9fA3wpPiExRXGIJ4aE4gJltl_1A/view?usp=sharing)
  
  
  ---
  
  