Answers.Body: <p>Remove the <code>--quiet</code> option, and capture STDERR as well as STDOUT:</p>
  <pre><code>bowtie2 -x human_mirs -U 1.lane.clean.gz -N 1 --norc --no-unal --no-head --ignore-quals 1&gt;sr1prueba.sam 2&gt;sr1prueba.summary.log
  </code></pre>
  <p><strong>See also:</strong></p>
  <p><a href="https://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#alignment-summary" rel="noreferrer"><code>bowtie2</code> manual: alignment summary</a></p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-10-18T21:09:21.823Z
Answers.LastActivityDate: 2023-10-18T21:09:21.823Z
Answers.UserDisplayName: Timur Shtatland
Answers.Body: <p>Get <a href="http://www.htslib.org/" rel="nofollow noreferrer">samtools</a>.</p>
  <p>Then run:</p>
  <pre><code>samtools stats file.bam
  </code></pre>
  <p>and/or</p>
  <pre><code>samtools flagstat file.bam
  </code></pre>
  <p>For example outputs see <a href="https://www.biostars.org/p/412621/" rel="nofollow noreferrer">here</a>.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-10-18T17:56:40.377Z
Answers.LastActivityDate: 2023-10-18T17:56:40.377Z
Answers.UserDisplayName: Maximilian Press
Body: <p>I am aligning my Small RNA Seq data with Bowtie 2. Although the alignment performs well, the only information I obtain after finishing running the alignment is the following:</p>
  <pre><code>## Time loading reference: 00:00:00
  ## Time loading forward index: 00:00:00
  ## Time loading mirror index: 00:00:00
  ## Multiseed full-index search: 00:00:00
  ## Time searching: 00:00:00
  ## Overall time: 00:00:00
  ## Time loading reference: 00:00:00
  ## Time loading forward index: 00:00:00
  ## Time loading mirror index: 00:00:00
  ## Multiseed full-index search: 00:00:01
  ## Time searching: 00:00:01
  ## Overall time: 00:00:01
  ## Time loading reference: 00:00:00
  ## Time loading forward index: 00:00:00
  ## Time loading mirror index: 00:00:00
  ## Multiseed full-index search: 00:00:00
  ## Time searching: 00:00:00
  ## Overall time: 00:00:00
  ## Time loading reference: 00:00:00
  ## Time loading forward index: 00:00:00
  ## Time loading mirror index: 00:00:00
  ## Multiseed full-index search: 00:00:00
  ## Time searching: 00:00:00
  ## Overall time: 00:00:00
  ## Time loading reference: 00:00:00
  ## Time loading forward index: 00:00:00
  ## Time loading mirror index: 00:00:00
  ## Multiseed full-index search: 00:00:00
  ## Time searching: 00:00:00
  ## Overall time: 00:00:00
  ## Time loading reference: 00:00:00
  ## Time loading forward index: 00:00:00
  ## Time loading mirror index: 00:00:00
  ## Multiseed full-index search: 00:00:00
  ## Time searching: 00:00:00
  ## Overall time: 00:00:00
  </code></pre>
  <p>This is my command line to build the index:
  bowtie2-build -o 3 -t 5 Nuevofastaorina human_mirs</p>
  <p>And this is my command line to do the alignment:</p>
  <pre><code>bowtie2 -x human_mirs -U 1.lane.clean.gz -N 1 --norc --no-unal --no-head --ignore-quals –-quiet &gt; sr1prueba.sam
  </code></pre>
  <p>Does anyone know how to obtain an alignment summary instead of the above information? What I mean by alignment summary is the following:</p>
  <pre><code>20000 reads; of these:
    20000 (100.00%) were unpaired; of these:
      1247 (6.24%) aligned 0 times
      18739 (93.69%) aligned exactly 1 time
      14 (0.07%) aligned &gt;1 times
  93.77% overall alignment rate
  </code></pre>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-10-19T03:21:15.310Z
Comments.Text: Please show the first few lines of your fastq input data (i.e. lane.clean.gz). This should help to diagnose the problem.
Comments.UserDisplayName: gringer
Tags: <rna-seq><phylogenetics><bowtie2>
Title: Cannot obtain alignment summary after running Bowtie2
ThreadText: # Cannot obtain alignment summary after running Bowtie2
  
  (Asked by: username_0 on 2023-10-18)
  
  I am aligning my Small RNA Seq data with Bowtie 2. Although the alignment performs well, the only information I obtain after finishing running the alignment is the following:
  
  ```
  ## Time loading reference: 00:00:00
  ## Time loading forward index: 00:00:00
  ## Time loading mirror index: 00:00:00
  ## Multiseed full-index search: 00:00:00
  ## Time searching: 00:00:00
  ## Overall time: 00:00:00
  ## Time loading reference: 00:00:00
  ## Time loading forward index: 00:00:00
  ## Time loading mirror index: 00:00:00
  ## Multiseed full-index search: 00:00:01
  ## Time searching: 00:00:01
  ## Overall time: 00:00:01
  ## Time loading reference: 00:00:00
  ## Time loading forward index: 00:00:00
  ## Time loading mirror index: 00:00:00
  ## Multiseed full-index search: 00:00:00
  ## Time searching: 00:00:00
  ## Overall time: 00:00:00
  ## Time loading reference: 00:00:00
  ## Time loading forward index: 00:00:00
  ## Time loading mirror index: 00:00:00
  ## Multiseed full-index search: 00:00:00
  ## Time searching: 00:00:00
  ## Overall time: 00:00:00
  ## Time loading reference: 00:00:00
  ## Time loading forward index: 00:00:00
  ## Time loading mirror index: 00:00:00
  ## Multiseed full-index search: 00:00:00
  ## Time searching: 00:00:00
  ## Overall time: 00:00:00
  ## Time loading reference: 00:00:00
  ## Time loading forward index: 00:00:00
  ## Time loading mirror index: 00:00:00
  ## Multiseed full-index search: 00:00:00
  ## Time searching: 00:00:00
  ## Overall time: 00:00:00
  
  ```
  
  This is my command line to build the index:
  bowtie2-build -o 3 -t 5 Nuevofastaorina human\_mirs
  
  And this is my command line to do the alignment:
  
  ```
  bowtie2 -x human_mirs -U 1.lane.clean.gz -N 1 --norc --no-unal --no-head --ignore-quals –-quiet > sr1prueba.sam
  
  ```
  
  Does anyone know how to obtain an alignment summary instead of the above information? What I mean by alignment summary is the following:
  
  ```
  20000 reads; of these:
    20000 (100.00%) were unpaired; of these:
      1247 (6.24%) aligned 0 times
      18739 (93.69%) aligned exactly 1 time
      14 (0.07%) aligned >1 times
  93.77% overall alignment rate
  
  ```
  
  **Tags:** rna-seq, phylogenetics, bowtie2
  
  > **Comments:**
  > **username_1**: Please show the first few lines of your fastq input data (i.e. lane.clean.gz). This should help to diagnose the problem.  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_2 on 2023-10-18. Score: 5
  
  Remove the `--quiet` option, and capture STDERR as well as STDOUT:
  
  ```
  bowtie2 -x human_mirs -U 1.lane.clean.gz -N 1 --norc --no-unal --no-head --ignore-quals 1>sr1prueba.sam 2>sr1prueba.summary.log
  
  ```
  
  **See also:**
  
  [`bowtie2` manual: alignment summary](https://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#alignment-summary)
  
  
  ---
  
  ### Answer by username_3 on 2023-10-18. Score: 2
  
  Get [samtools](http://www.htslib.org/).
  
  Then run:
  
  ```
  samtools stats file.bam
  
  ```
  
  and/or
  
  ```
  samtools flagstat file.bam
  
  ```
  
  For example outputs see [here](https://www.biostars.org/p/412621/).
  
  
  ---
  
  