How to calculate the depth of nanopore reads in IGV

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2.0 years ago

kirankumareripogu ▴ 10

Hi,

I wanted to see what is the depth of the nanopore reads in IGV.

I used bwa (Burrow-Wheeler Aligner) to map the raw nanopore reads to the reference genome and saved it as ban file. Then, I used samtools to convert the bam file into sam so that I can view it using IGV.

I have the IGV documentation, but failed to understand how do I know what is the depth of the nanopore reads. Is there a way that I can know the depth using the IGV settings in the menu panel?

Thank you..

Kiran enter image description here

IGV Depth Nanopore • 1.2k views

ADD COMMENT • link 2.0 years ago by kirankumareripogu ▴ 10

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You don't have to convert bam to sam to use IGV. IGV is a visualization tool, not optimal to calculate things like coverage. For that I would use mosdepth.

ADD REPLY • link 2.0 years ago by WouterDeCoster 47k

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@WouterDeCoster Thank you so much for your reply.

ADD REPLY • link 2.0 years ago by kirankumareripogu ▴ 10

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