viewing alignment to find deletions

[linda...@gmail.com]

I want to find any deletions from my bam files. According to your tutorial, I can see it based on the colors if set

Color alignments>by insert size in the popup menu. But there’s no choice for ‘insert size’ under 'Color alignments by’. The version of IGV I am using is 2.4.19. Could you tell me what’s wrong here?

[James Robinson]

That only applies to paired end alignments, and your alignments are not paired end.  They look like pacbio.    I suggest you watch this tutorial,  the title says "IGV 3" but it applies to this version:  https://www.pacb.com/blog/igv-3-improves-support-pacbio-long-reads/

Further,  you really can't rely on a visual program like IGV to find your deletions,  you need to do a proper analysis.  IGV can help confirm the analysis,  but its not primarily an analysis tool.

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[linda...@gmail.com]

Hi James,

Thanks for your help! It's pacbio. I am new to this. Could you give me any suggestions about analysis tools suitable for finding deletions or insertions from Pacbio genomic ccs reads or its aligned bam file?

Thanks,

Xue

[James Robinson]

No sorry,  try some BioStars or SeqAnswers,  or PacBio support.

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[Malcolm Cook]

Xue - you might well wind up using GATK - see https://gatkforums.broadinstitute.org/gatk/discussions/tagged/pacbio/p1 for tips on using it with pacbio data