few matched barcodes between HTO and RNA libraries after using V3 mapped whitelist

[lb15]

Hi,

I ran cite-seq count on cell hashing data using the whitelist from the cellranger filtered output. Since it's 10X V3 data, I mapped the cellranger filtered output barcodes to the 10X genomics whitelist, as suggested, and used that for the -wl option, along with -cells 0 option.

I get back ~81% mapped reads and a matrix with the same number of barcodes as the filtered data. I would expect that these barcodes match. However, when I use Seurat Cell Hashing tutorial to read in the HTO and filtered matrix (I remove the tailing -1), only 14 barcodes intersect.

Do I need to translate the filtered matrix from the RNA library in order to match to the HTOs? I was under the impression this would only be required for the whitelist. If so, do you have a recommendation of how to do that? I'm not exactly sure what this translation is doing or have a file that has old and translated barcodes to match and replace.

Thanks!

[Hoohm]

Hello @lb15 yes, there is a translation required.

You could use this small script I wrote to help out https://gist.github.com/Hoohm/edf05b544105cd3f396d6e8c5dd66b22

Let me know if it works for you.

I'm struggling to work on the new release but it will do the translation on the fly for you :)

[Hoohm]

Hello @lb15 I have great news about this issue. The new release, 1.5.0, which should come out tomorrow now does the translation for you if you provide the barcode list with both barcodes. This means that your cells will match directly out of the box without having to deal with it.