<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>

CC BY-SA 4.0
2022-08-14T04:02:29.477Z
2022-08-14T04:02:29.477Z
envs_h_gang_5
<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>

CC BY-SA 4.0
2022-08-14T04:48:09.160Z
2022-08-14T04:48:09.160Z
user172818
<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>

<phylogenetics><bowtie2><star>
STAR vs Bowtie2
# 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)


---

