<p>You should just open the bam file, not one of the index files.</p>

CC BY-SA 4.0
2024-06-14T06:49:21.280Z
2024-06-14T06:49:21.280Z
Wouter De Coster
<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>

CC BY-SA 4.0
2024-06-14T09:21:55.150Z
What file did you open? Have you tried opening the .bam file?
terdon
<long-reads><pacbio>
how to see pacbio reads in IGV
# 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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