how to see Pacbio reads in IGV

Question

[María José]

HI,

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 lectures. Could you recommend other tools??

[Pierre Lindenbaum]

cross posted: https://bioinformatics.stackexchange.com/questions/22609

Do not post on multiple forums - that is just bad etiquette. What's worse, you did not link between the two so no one knows that you're asking two sets of online volunteers to spend their time on your problem without telling them that you're also asking the other group.

Answer 1

[Billy Rowell]

The alignments are in the .bam file, and the .bam.bai and .bam.pbi are two kinds of indices for the BAM. Try loading the .bam in IGV.