<p>Bowtie is providing you with the index files for hg38.  This are the result of the <a href="http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#the-bowtie2-build-indexer" rel="nofollow noreferrer">bowtie2-build indexer</a>.  However you have downloaded the indexes for Bowtie1 not bowtie2</p>

<blockquote>
  <p>Bowtie 2’s .bt2 index format is different from Bowtie 1’s .ebwt
  format, and they are not compatible with each other.</p>
</blockquote>

<p>Then according to the <a href="http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#command-line" rel="nofollow noreferrer">manual</a> you pass the basename of the index for the reference genome. So this should be the name prior to the extension, .1.bt2 for Bowtie2.</p>

<pre><code>bowtie2 [options]* -x &lt;bt2-idx&gt; {-1 &lt;m1&gt; -2 &lt;m2&gt; | -U &lt;r&gt; | --interleaved &lt;i&gt;} -S [&lt;sam&gt;]
Main arguments
-x &lt;bt2-idx&gt;
The basename of the index for the reference genome. The basename is the name of any of the index files up to but not including the final .1.bt2 / .rev.1.bt2 / etc. bowtie2 looks for the specified index first in the current directory, then in the directory specified in the BOWTIE2_INDEXES environment variable.
</code></pre>

CC BY-SA 4.0
2019-01-31T22:01:43.393Z
2019-01-31T22:01:43.393Z
Bioathlete
<p>I downloaded the H. sapiens, NCBI GRCh38 files from Bowtie's website. After unzipping, there are 6 files, 4 that end in set 1.ebwt, set2.ebwt, set3.ebwt, and set4.ebwt and two that end in set.rev.1.ebwt and set.rev.2.ebwt. </p>

<p>I am unable to find any explanation for what these files are either online.</p>

<p>which one do I use for bowtie2 mapping?</p>

<p>Thanks</p>

<phylogenetics><genome><human><bowtie2>
Seeking explanation of the hg38 files downloaded from bowtie 2 website
# Seeking explanation of the hg38 files downloaded from bowtie 2 website

(Asked by: username_0 on 2019-01-31)

I downloaded the H. sapiens, NCBI GRCh38 files from Bowtie's website. After unzipping, there are 6 files, 4 that end in set 1.ebwt, set2.ebwt, set3.ebwt, and set4.ebwt and two that end in set.rev.1.ebwt and set.rev.2.ebwt.

I am unable to find any explanation for what these files are either online.

which one do I use for bowtie2 mapping?

Thanks

**Tags:** phylogenetics, genome, human, bowtie2

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## 1 answers

### Answer by username_1 on 2019-01-31. Score: 3

Bowtie is providing you with the index files for hg38.  This are the result of the bowtie2-build indexer.  However you have downloaded the indexes for Bowtie1 not bowtie2

Bowtie 2’s .bt2 index format is different from Bowtie 1’s .ebwt
  format, and they are not compatible with each other.

Then according to the manual you pass the basename of the index for the reference genome. So this should be the name prior to the extension, .1.bt2 for Bowtie2.
bowtie2 [options]* -x  {-1  -2  | -U  | --interleaved } -S []
Main arguments
-x 
The basename of the index for the reference genome. The basename is the name of any of the index files up to but not including the final .1.bt2 / .rev.1.bt2 / etc. bowtie2 looks for the specified index first in the current directory, then in the directory specified in the BOWTIE2_INDEXES environment variable.


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