numbatm vignette #231
numbatm vignette #231
Conversation
|
|
||
| # Introduction | ||
|
|
||
| This vignette provides a guide to preparing input data for running Numbat-multiome. |
There was a problem hiding this comment.
I would emphasize ATAC mode here as well, since many people are trying to use the ATAC-only mode
| ### Generate gene-to-bin mapping | ||
|
|
||
| ```bash | ||
| binGR="var220kb.rds" # path to grange object containing genomic bins |
There was a problem hiding this comment.
Could you provide this RDS file to the user? Like giving a download link? Otherwise not everyone knows how to generate this properly
|
|
||
| ```bash | ||
| binGR="var220kb.rds" # path to grange object containing genomic bins | ||
| gtfF="gtf_hg38.gtf" # any version of gtf files you use or hg38, hg19 or mm10 |
There was a problem hiding this comment.
Is this the numbat gtf_hg38? dataframe saved as a flat file? Please also give download link
|
|
||
| ```bash | ||
| binGR="var220kb.rds" | ||
| Rscript get_binned_rna.R \ |
There was a problem hiding this comment.
Please explain more about the types of input accepted in this get_binned_rna.R script. For example --rnaCountsFile could be a h5 file or seurat object. Would be useful to explain this here. Same for the other arguments and for the get_binned_atac.R script
| ### Generate binned ATAC counts | ||
|
|
||
| ```bash | ||
| Rscript get_binned_atac.R \ |
There was a problem hiding this comment.
Add argument description here
|
|
||
| ```r | ||
| saveRDS(binCnt(c(glue("${sample}/{sample}_rna_bin.rds"), | ||
| glue("${sample}/{sample}_atac_bin.rds")),123), |
| ### Generate combined count matrix | ||
|
|
||
| ```r | ||
| saveRDS(binCnt(c(glue("${sample}/{sample}_rna_bin.rds"), |
There was a problem hiding this comment.
A bit confusing here, could you break it down more on how you go in an interactive R session, load the bin.rds objects, run binCnt, and then save the combined bin count?
| saveRDS(ref_comb, "Reference/lambdas_comb_bincnt.rds") | ||
| ``` | ||
|
|
||
| ## 4. Compile and run |
There was a problem hiding this comment.
"Compile" reminds me of C++ stuff, but there's no compilation here
|
|
||
| # ATAC-bin and RNA-bin modes | ||
|
|
||
| If you want to run Numbat-multiome in RNA bin and ATAC bin modes, you can simply use `lambdas_RNA_bincnt.rds` and `lambdas_ATAC_bincnt.rds` as the reference files. `${sample}_rna_bin.rds` and `${sample}_atac_bin.tsv` as the count matrix. |
There was a problem hiding this comment.
Could you expand more on running in ATAC-only mode? That would be very useful. Right now this is not clear
There was a problem hiding this comment.
I would also separate the RNA and ATAC instruction here
2 participants
No description provided.