Formatting errors

[joebielanski]

Hello! I'm trying to take a Seurat object made up of 15 samples and explore it in Loupe after I processed, filtered and integrated it in R. Upon running create_loupe() or create_loupe_from_seurat() I get the following errors:

2024/04/15 15:05:07 validating count matrix
Error in create_loupe(count_mat = count_mat, clusters = clusters, projections = projections,  : 
  
It looks like the formatting of your count matrix does not match the required formatting for LoupeR. For further information, please see the documentation: 10xgen.com/louper

There is an issue with the formatting of your barcodes. Barcodes should begin with base pairs and end with an optional hyphen and suffix. For further information, please see the documentation: 10xgen.com/louper

I've explored the documentation and there really isn't anything explaining this error/what the required format is even supposed to be, so I'm quite lost.

could it be that my barcodes, each coming from 1 of 15 samples have the name attached to them at the front of the barcode? eg// 'Fox12-21_AAACCCACAACGCACAG-1' is my first. That's just the default though. I haven't done anything to mess with them. Any advice on how to proceed is much appreicated.

[esiegel]

You can try modifying the barcodes to have the ACTGs first and then a hyphen and whatever suffix you like. Do note that the data must come from a 10x experiment

[joebielanski]

Thanks! I'll give that a go and try swapping the IDs and the sequences itself. All the data is from 15 separate 10x experiments we did ourselves so there's no worry there. Something in our analysis pipeline, built for older versions of Seurat may have changed stuff up a bit.

[josegarciamanteiga]

Hi,
Did you manage to solve the issue? I have I think the same, but I already have the correct barcode formats and the error is always the same. Thanks!