Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-01-31T22:01:43.393Z
Answers.LastActivityDate: 2019-01-31T22:01:43.393Z
Answers.UserDisplayName: Bioathlete
Body: <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>
  
Tags: <phylogenetics><genome><human><bowtie2>
Title: Seeking explanation of the hg38 files downloaded from bowtie 2 website
ThreadText: # 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
  
  
  ---
  
  ## 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](http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#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](http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#command-line) 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 <bt2-idx> {-1 <m1> -2 <m2> | -U <r> | --interleaved <i>} -S [<sam>]
  Main arguments
  -x <bt2-idx>
  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.
  
  ```
  
  
  ---
  
  