Error in addGeneExpressionMatrix(input = projMulti2, seRNA = seRNA, strictMatch = FALSE, : Detected less than 50% of seqnames for seRNA in chromSizes! Are you sure the seqnames of your seRNA are correct?!

[sylestiel]

@rcorces, @archrdevs

Please help me troubleshoot the error obtained at the addgeneExpressionMatrix step. Unable to get past this issue.

For createGeneAnnotation function in ArchR what would be the appropriate dataset and steps to go with BSgenome.Mmulatta.UCSC.rheMac10?

I tried
geneAnnotation <- createGeneAnnotation(TxDb = TxDb.Mmulatta.UCSC.rheMac10.refGene, OrgDb = org.Mmu.eg.db)
However, I'm not sure if that is correct.
The output read as follows:
Getting Genes..
29 genes were dropped because they have exons located on both strands of
the same reference sequence or on more than one reference sequence, so
cannot be represented by a single genomic range.
Use 'single.strand.genes.only=FALSE' to get all the genes in a GRangesList
object, or use suppressMessages() to suppress this message.

Determined Annotation Style = ENTREZID

Getting Exons..
Getting TSS..

Further along I encountered problems with
proj <-addGeneExpressionMatrix(input=proj, seRNA=seRNA, force= TRUE) step.
This makes me wonder if there is something amiss with my approach.

Error in addGeneExpressionMatrix(input = proj, seRNA = seRNA, force = TRUE) :

Detected less than 50% of seqnames for seRNA in chromSizes! Are you sure the seqnames of your seRNA are correct?!

I would really appreciate your suggestions.

Thanks!

[sylestiel]

@rcorces
Just happened to stumble upon your updated vignette for Multiomic Data Analysis. Problem has NOT resolved.

projMulti2 <- addGeneExpressionMatrix(input = projMulti2, seRNA = seRNA,strictMatch = FALSE, force = TRUE)

ArchR logging to : ArchRLogs/ArchR-addGeneExpressionMatrix-9b615327254-Date-2023-11-08_Time-16-05-08.227282.log
If there is an issue, please report to github with logFile!
Error in addGeneExpressionMatrix(input = projMulti2, seRNA = seRNA, strictMatch = FALSE, :
Detected less than 50% of seqnames for seRNA in chromSizes! Are you sure the seqnames of your seRNA are correct?!

[sylestiel]

@rcorces

Hi Ryan,

I really need some help to get past this issue. Pretty stuck at this point.