Answers.Body: <p>You should just open the bam file, not one of the index files.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-06-14T06:49:21.280Z
Answers.LastActivityDate: 2024-06-14T06:49:21.280Z
Answers.UserDisplayName: Wouter De Coster
Body: <p><em>This question has also been asked on <a href="https://www.biostars.org/p/9596968/#9596989" rel="nofollow noreferrer">Biostars</a></em></p>
  <p>I recently used pbmm2 to align my reads to the reference genome, when I specified  --sort option it is generated a file with extension bam.bai. Afterwards, an index with extension .bam.pbi was generated with pbindex. IGV could not open .bam.pbi, so I tried with bam.bai. The first time I could see the mapping, but I have tried the same steps as the first time and I cannot see the coverage of the reads.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-06-14T09:21:55.150Z
Comments.Text: What file did you open? Have you tried opening the .bam file?
Comments.UserDisplayName: terdon
Tags: <long-reads><pacbio>
Title: how to see pacbio reads in IGV
ThreadText: # how to see pacbio reads in IGV
  
  (Asked by: username_0 on 2024-06-13)
  
  *This question has also been asked on [Biostars](https://www.biostars.org/p/9596968/#9596989)*
  
  I recently used pbmm2 to align my reads to the reference genome, when I specified --sort option it is generated a file with extension bam.bai. Afterwards, an index with extension .bam.pbi was generated with pbindex. IGV could not open .bam.pbi, so I tried with bam.bai. The first time I could see the mapping, but I have tried the same steps as the first time and I cannot see the coverage of the reads.
  
  **Tags:** long-reads, pacbio
  
  > **Comments:**
  > **username_1**: What file did you open? Have you tried opening the .bam file?  
  
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  ## 1 answers
  
  ### Answer by username_2 on 2024-06-14. Score: 4
  
  You should just open the bam file, not one of the index files.
  
  
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