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

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

cellranger deeptools bigwig igv single-cell
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updated by Ram Ram • written by bioyas • bioyas

1 answer

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.

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written by jared.andrews07 jared.andrews07

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.

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written by bioyas • 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.

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written by bioyas • bioyas

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.

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written by jared.andrews07 jared.andrews07

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