Answers.Body: <p>You are looking for <code>bedtools genomecov</code>, specifically <a href="https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html#d-reporting-per-base-genome-coverage" rel="nofollow noreferrer"><code>-d</code></a> option. See <a href="https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html" rel="nofollow noreferrer">https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html</a> , for example:</p>
  
  <pre><code>bedtools genomecov -i A.bed -g my.genome -d
  </code></pre>
  
  <hr>
  
  <p>I recommend not reinventing the wheel: use <code>bedtools</code> instead of reimplementing the same functionality in Perl.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-01-28T14:21:11.230Z
Answers.Text: thanks, but bedtools doesn't work in this case as there is no header info.
Answers.UserDisplayName: Gene_of_Thrones
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-01-28T14:25:52.557Z
Answers.Text: Can you add it from another bam file using samtools? Or add a fake header?
Answers.UserDisplayName: Timur Shtatland
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-02-10T13:14:16.093Z
Answers.Text: i did add a header from a different sample to calculate the coverage... just wondering if we can do it using awk.
Answers.UserDisplayName: Gene_of_Thrones
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-01-27T17:39:13.583Z
Answers.LastActivityDate: 2020-01-27T17:39:13.583Z
Answers.UserDisplayName: Timur Shtatland
Body: <p>I have a RNA aligned file without any header info. 
  I need to calculate the coverage of each mapped base for per chromosome. Is it possible to do it with perl ? </p>
  
  <pre><code>NS500377:28:H16A7BGXX:2:21205:16038:7658        99      chr2   3000482 255     46M     =       3000502 56      GTCCTACAGTGTGCATTTCTCGTTTTCCACGTTTCT    AAAA)FFFFFFFFFAFFFFFFFFFFF.F.FFFFFAF    XA:i:2  MD:Z:21T4T7T1   NM:i:3
  NS500377:28:H16A7BGXX:3:11503:24953:10427       99      chr2   3000482 255     50M     =       3000513 71      GTCCTACAGTGTGCATTTCTCATTTTTCAAGTTTTTCAGT        AAAAAFFFFFFFFFFFFAFFFFFF7AAFFFFFFFFFFFFF
          XA:i:1  MD:Z:21T7C10    NM:i:2
  NS500377:28:H16A7BGXX:3:12404:23929:9392        163     chr2   3000482 255     49M     =       3000483 40      GTCCTACAGTGTGCATTTCCCTTTTTTCACGTTTTTTAG AAFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF XA:i:1  MD:Z:19T16C2    NM:i:2
  NS500377:28:H16A7BGXX:3:12404:23929:9392        83      chr2   3000483 255     49M     =       3000482 -40     TCCTACAGTGTGCATTTCCCTTTTTTCACGTTTTTTAGT AFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF XA:i:2  MD:Z:18T16C3    NM:i:2
  NS500377:28:H16A7BGXX:3:21606:15675:1639        83      chr2   3000483 255     50M     =       3000480 -43     TCTTACAGTGTGCATTTCTCTTTTTTCACGTTTTTCAGTG        AFFFFFFFFFAFFFFFFFFFFFFFFFFFFFFFFFFAAAAA
          XA:i:0  MD:Z:2C37       NM:i:1
  NS500377:28:H16A7BGXX:4:12605:18505:11088       83      chr2   3000486 255     50M     =       3000481 -45     TACAATGTGCATTTCTCTTTTTTCACGTTTTTCAGTATTT        FFFFFFFAFFF)FFFFFFFFF&lt;FFFF&lt;AFFFFFFFAA&lt;AA
          XA:i:1  MD:Z:4G31G3     NM:i:2
  NS500377:28:H16A7BGXX:2:13303:20634:12085       99      chr2   3000487 255     49M     =       3000521 73      ACAGTGTACATTTCTCATTTTTCACGTTTTTCAGTGTTA AAAAAFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF. XA:i:2  MD:Z:7G8T21T0   NM:i:3
  </code></pre>
  
Tags: <rna><coverage><awk>
Title: how to calculate coverage of each base of mapped reads?
ThreadText: # how to calculate coverage of each base of mapped reads?
  
  (Asked by: username_0 on 2020-01-27)
  
  I have a RNA aligned file without any header info.
  I need to calculate the coverage of each mapped base for per chromosome. Is it possible to do it with perl ?
  
  ```
  NS500377:28:H16A7BGXX:2:21205:16038:7658        99      chr2   3000482 255     46M     =       3000502 56      GTCCTACAGTGTGCATTTCTCGTTTTCCACGTTTCT    AAAA)FFFFFFFFFAFFFFFFFFFFF.F.FFFFFAF    XA:i:2  MD:Z:21T4T7T1   NM:i:3
  NS500377:28:H16A7BGXX:3:11503:24953:10427       99      chr2   3000482 255     50M     =       3000513 71      GTCCTACAGTGTGCATTTCTCATTTTTCAAGTTTTTCAGT        AAAAAFFFFFFFFFFFFAFFFFFF7AAFFFFFFFFFFFFF
          XA:i:1  MD:Z:21T7C10    NM:i:2
  NS500377:28:H16A7BGXX:3:12404:23929:9392        163     chr2   3000482 255     49M     =       3000483 40      GTCCTACAGTGTGCATTTCCCTTTTTTCACGTTTTTTAG AAFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF XA:i:1  MD:Z:19T16C2    NM:i:2
  NS500377:28:H16A7BGXX:3:12404:23929:9392        83      chr2   3000483 255     49M     =       3000482 -40     TCCTACAGTGTGCATTTCCCTTTTTTCACGTTTTTTAGT AFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF XA:i:2  MD:Z:18T16C3    NM:i:2
  NS500377:28:H16A7BGXX:3:21606:15675:1639        83      chr2   3000483 255     50M     =       3000480 -43     TCTTACAGTGTGCATTTCTCTTTTTTCACGTTTTTCAGTG        AFFFFFFFFFAFFFFFFFFFFFFFFFFFFFFFFFFAAAAA
          XA:i:0  MD:Z:2C37       NM:i:1
  NS500377:28:H16A7BGXX:4:12605:18505:11088       83      chr2   3000486 255     50M     =       3000481 -45     TACAATGTGCATTTCTCTTTTTTCACGTTTTTCAGTATTT        FFFFFFFAFFF)FFFFFFFFF<FFFF<AFFFFFFFAA<AA
          XA:i:1  MD:Z:4G31G3     NM:i:2
  NS500377:28:H16A7BGXX:2:13303:20634:12085       99      chr2   3000487 255     49M     =       3000521 73      ACAGTGTACATTTCTCATTTTTCACGTTTTTCAGTGTTA AAAAAFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF. XA:i:2  MD:Z:7G8T21T0   NM:i:3
  
  ```
  
  **Tags:** rna, coverage, awk
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2020-01-27. Score: 1
  
  You are looking for `bedtools genomecov`, specifically [`-d`](https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html#d-reporting-per-base-genome-coverage) option. See <https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html> , for example:
  
  ```
  bedtools genomecov -i A.bed -g my.genome -d
  
  ```
  
  ---
  
  I recommend not reinventing the wheel: use `bedtools` instead of reimplementing the same functionality in Perl.
  
  > **Comments:**
  > **username_0**: thanks, but bedtools doesn't work in this case as there is no header info.  
  > **username_1**: Can you add it from another bam file using samtools? Or add a fake header?  
  > **username_0**: i did add a header from a different sample to calculate the coverage... just wondering if we can do it using awk.  
  
  ---
  
  