Error Loading CellBender v3alpha H5 output in R
See original GitHub issueHi,
First thanks so much for developing and updating this awesome software! I have been using v2 on Terra for some time and recently saw v3alpha and decided to give that a go (Additional html report is awesome!). However, I’m running into issue loading the data in R using Seurat. Previously I could use Seurat’s Read10X_h5
command. However, now when I do that (either with filtered or full .h5 files I get the following error:
test <- Read10X_h5("/PATH/SampleB_CB_out.h5", use.names = T)
Error in `[[.H5File`(infile, paste0(genome, "/data")) :
An object with name droplet_latents/data does not exist in this group
I saw a note in another issue about output of h5 file changing with v3 but didn’t detail how. What is best way to load the v3alpha h5 files in R?
Thanks! Sam
Issue Analytics
- State:
- Created a year ago
- Comments:6 (1 by maintainers)
Top Results From Across the Web
ERROR reading h5 output in R · Issue #45 - GitHub
I can successfully read the output files with read10xCounts() ... 3) library library(Seurat) # load data from the filtered h5 file data.file ...
Read more >Usage - CellBender documentation - Read the Docs
The output of remove-background includes a new .h5 count matrix, with background RNA removed, that can directly be used in downstream analysis in...
Read more >Background Removal Guidance for Single Cell Gene ...
Load the raw feature barcode matrix file from your cellranger output using the command below. cellbender remove-background \ --input ...
Read more >Error Loading CellBender v3alpha H5 output in R - IssueHint
I saw a note in another issue about output of h5 file changing with v3 but didn't detail how. What is best way...
Read more >Read & Write Data Functions • scCustomize
Starting with CellBender v3 the output file is styled like Cell Ranger h5 files it also contains some additional information.
Read more >Top Related Medium Post
No results found
Top Related StackOverflow Question
No results found
Troubleshoot Live Code
Lightrun enables developers to add logs, metrics and snapshots to live code - no restarts or redeploys required.
Start FreeTop Related Reddit Thread
No results found
Top Related Hackernoon Post
No results found
Top Related Tweet
No results found
Top Related Dev.to Post
No results found
Top Related Hashnode Post
No results found
Top GitHub Comments
Hey @sjfleming Sorry for delayed response! Yes V3 alpha seemed to run without any issues (running on Terra)!
I think I will try and submit the primary function to SeuratWrappers in near future (that seems to be their rec for adding new import functions for other formats).
I’ve also created both multi directory and multi-file wrappers in scCustomize as well to read in files from whole experiment (stored in subdirectories or just within one directory) to make things easy for large experiments and add parallelization for additional speed (even though hdf5 files are already pretty quick).
Also added support for examining feature level changes within a dual assay Seurat object https://github.com/samuel-marsh/scCustomize/issues/70#issuecomment-1304047416 (matrix to matrix version coming) (side note it’s great to have this already included in new v3 html report). So this just provides easy wrapper to examine within R/Seurat.
Best, Sam
Hi,
As fyi, to simplify things on the R end for users I just wrote helper function for my package, scCustomize, to load the counts matrix from new CellBender outputs entirely within R without requiring PyTables. It’s basically slimmed version of
Seurat::Read10X_h5
that only reads the matrix.https://github.com/samuel-marsh/scCustomize/blob/58529b4dc870860c64d5c96eb078f353d7c4ca2b/R/Read_%26_Write_Data.R#L1054
I may update function name and will add it to my other scCustomize CellBender functions vignette. Planning v0.8.0 release for scCustomize by end of the month at latest.
Thanks again, Sam