text: user6273: I am using bedtools coverage to compute the sequencing depth at every positions of a chromosome but it didn't work as I expected.
  Instead it reported 0 coverage at every positions.
  This is how I did it :
  I made a chr1.bed bedfile :
  chr start   end 
  1   1   158534110
  
  I ran this command  :
  coverageBed -a -d chr1.bed -b aln.bam -s > coverage.perposition_chr1.tsv
  
  However I don't find any position in the output that is actually covered :
  chr start end 1-pos depth
  1   1   158534110   1   0
  1   1   158534110   2   0
  1   1   158534110   3   0
  1   1   158534110   4   0
  1   1   158534110   5   0
  1   1   158534110   6   0
  1   1   158534110   7   0
  1   1   158534110   8   0
  (...)
  1   1   158534110   158534109   0
  
  
  I must do something wrong because I already computed depth at specific pattern positions using the same aln.bam and it was working fine...
  Suggestions and tries :
  
  Swapping -a & -d parameters produces the same results
  Adding a strand column to the bedfile still gives 0 coverage.
  
  chr1.bed
  1       1       158534110       .       0       +
  1       1       158534110       .       0       -
  
  output
  
  1       1       158534110       .       0       +       1       0
  1       1       158534110       .       0       +       2       0
  (...)
  1       1       158534110       .       0       -       158534108       0
  1       1       158534110       .       0       -       158534109       0
  ```
  
  
  user16501: If you prefer to have a more concise report than a per-base one, bedtools genomecov could be a better choice.
  Its -bga option allows you to report consecutive bases that have the same coverage as a range in a single line.
  In your case, you could achieve this (unfortunately they only offer the strandedness option for a specified strand) by running the following command:
  bedtools genomecov -bga -ibam aln.bam -g chr1.bed -strand + > coverage.perposition_chr1.tsv
  
  Output will look like:
  chr1  554304  554309  5
  chr1  554309  554313  6
  chr1  554313  554314  1
  chr1  554315  554316  6
  chr1  554316  554317  5
  
  
original_text: 6273: <p>I am using bedtools coverage to compute the sequencing depth at every positions of a chromosome but it didn't work as I expected.
  Instead it reported 0 coverage at every positions.</p>
  <p>This is how I did it :</p>
  <p>I made a <code>chr1.bed</code> bedfile :</p>
  <pre><code>chr start   end 
  1   1   158534110
  </code></pre>
  <p>I ran this command  :</p>
  <pre><code>coverageBed -a -d chr1.bed -b aln.bam -s &gt; coverage.perposition_chr1.tsv
  </code></pre>
  <p>However I don't find any position in the output that is actually covered :</p>
  <pre><code>chr start end 1-pos depth
  1   1   158534110   1   0
  1   1   158534110   2   0
  1   1   158534110   3   0
  1   1   158534110   4   0
  1   1   158534110   5   0
  1   1   158534110   6   0
  1   1   158534110   7   0
  1   1   158534110   8   0
  (...)
  1   1   158534110   158534109   0
  
  </code></pre>
  <p>I must do something wrong because I already computed depth at specific pattern positions using the same <code>aln.bam</code> and it was working fine...</p>
  <p><strong>Suggestions and tries :</strong></p>
  <ul>
  <li>Swapping <code>-a</code> &amp; <code>-d</code> parameters produces the same results</li>
  <li>Adding a strand column to the bedfile still gives 0 coverage.</li>
  </ul>
  <p><code>chr1.bed</code></p>
  <pre><code>1       1       158534110       .       0       +
  1       1       158534110       .       0       -
  </code></pre>
  <p><code>output</code></p>
  <pre><code>
  1       1       158534110       .       0       +       1       0
  1       1       158534110       .       0       +       2       0
  (...)
  1       1       158534110       .       0       -       158534108       0
  1       1       158534110       .       0       -       158534109       0
  <span class="math-container">```</span>
  </code></pre>
   16501: <p>If you prefer to have a more concise report than a per-base one, <a href="https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html" rel="nofollow noreferrer">bedtools genomecov</a> could be a better choice.</p>
  <p>Its <code>-bga</code> option allows you to report consecutive bases that have the same coverage as a range in a single line.</p>
  <p>In your case, you could achieve this (unfortunately they only offer the strandedness option for a specified strand) by running the following command:</p>
  <pre><code>bedtools genomecov -bga -ibam aln.bam -g chr1.bed -strand + &gt; coverage.perposition_chr1.tsv
  </code></pre>
  <p>Output will look like:</p>
  <pre><code>chr1  554304  554309  5
  chr1  554309  554313  6
  chr1  554313  554314  1
  chr1  554315  554316  6
  chr1  554316  554317  5
  </code></pre>
  