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MarioniLab / DropletUtils

Clone of the Bioconductor repository for the DropletUtils package.
https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html
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using read10xMolInfo (v1.14.0 for h5 files from v1.6.1 #81

Open chensujun opened 2 years ago

chensujun commented 2 years ago

Hi Aaron,

I was trying to run QC using the latest DropletUtils but the h5 files were generated with older versions of tools and failed to be read in by the newer read10xMolInfo function. Is there a way to deal with it?

Best, Sujun

jonathangriffiths commented 2 years ago

Hi Sujun,

Do you mean that the h5 files are from an older version of cellranger?

Jonny

chensujun commented 2 years ago

Hi Jonny,

Thanks for getting back to me. No it's not from cellranger. The h5 was customized to work with DropletUtils v1.6.1. And problem with the newer version is that it requires 'library_idx', which wasn't there when generating the file.

Best, Sujun

jonathangriffiths commented 2 years ago

Are you saying you have customised the h5 file?

You could further customise it to add the library_idx information following the documentation from 10X, here.

chensujun commented 2 years ago

Thanks Jonny! Yes someone else customized the h5 file. I was just wondering if there's a way to make the old function compatible with the new version of tools. But you are right, perhaps modify those files is more feasible.

jonathangriffiths commented 2 years ago

You could try installing an old version of the software!

I haven't followed along with the history of these file formats though, so I'm afraid I can't pinpoint a version for you