Loading possorted_genome_bam.bam generated by 10X cellranger count command into IGV.

Question

[bioyas]

Hi,

I would like to look at the sorted bam file outputted from count command from Cellranger. When I try to load the bam file into IGV, it takes couple of minutes to load the reads and even after that no pile up is shown in the IGV track. I thought that might be related to the size of bam file (~ 10 GB). So I was wondering if I can use bamCoverage command from deeptools package to convert the possorted_genome_bam.bam to bigwig format.

Do you think that could resolve the issue?

Thanks

Answer 1

[jared.andrews07]

Zoom in on a specific region and ensure you're using the proper genome build. It will load only the reads in view if you zoom into a reasonably sized region.

[bioyas]

Thank you Jared. I zoomed in and it shows the pile up. Anyway Can I convert the bam to bigwig file using deeptools bamCoverage tool which make the file smaller.

[jared.andrews07]

Sure, if you want.

[bioyas]

Actually, I am using the following command from deeptools package to convert my sorted bam files to bigwig format to have smaller files that I can easily load into IGV.

bamCoverage --bam Sample.sorted.bam -o Sample.bw

I loaded both sorted.bam and bigwig file into IGV tool and I noticed that bigwig track doesn't show the pileups as they are in bam track. Do you have any idea what can go wrong? I need to do this as I have several samples and the sorted bam files are large and cannot store them on my local machine.

Appreciate your help.

[jared.andrews07]

Can't really help with no error or anything. How large is the resulting bigwig? Again, IGV doesn't render coverage unless zoomed in, so be sure you are zoomed in on a specific region.