TSS Enrichment error in Signac
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9 weeks ago
kousi31 ▴ 100

I downloaded .h5 matrix files from GEO website and I am learning scATAC-Seq. I got error while calculating TSS Enrichment score.

>   merged_seurat <- TSSEnrichment(object = merged_seurat, fast = FALSE)
Extracting TSS positions
Finding + strand cut sites
Finding - strand cut sites
Error in `colnames<-`(`*tmp*`, value = seq_len(length.out = region.width) -  : 
  attempt to set 'colnames' on an object with less than two dimensions

When I searched for the error I got to know that annotation version used maybe different.

I checked seqlevels(seurat_obj)

 seqlevels(merged_seurat)
  [1] "chr1"                    "chr2"                    "chr3"                    "chr4"                   
  [5] "chr5"                    "chr6"                    "chr7"                    "chr8"                   
  [9] "chr9"                    "chr10"                   "chr11"                   "chr12"                  
 [13] "chr13"                   "chr14"                   "chr15"                   "chr16"                  
 [17] "chr17"                   "chr18"                   "chr19"                   "chr20"                  
 [21] "chr21"                   "chr22"                   "chrX"                    "chrY"                   
 [25] "chrM"                    "chr1_GL383518v1_alt"     "chr1_GL383519v1_alt"     "chr1_GL383520v2_alt"    
 [29] "chr1_KI270759v1_alt"     "chr1_KI270760v1_alt"     "chr1_KI270761v1_alt"

I had "chr1_KI270759v1_alt" and so on..

seqlevels(annotations) did not have these seqlevels.
I tried using EnsDb.Hsapiens.v86 and EnsDb.Hsapiens.v111. Both did not have the "extra" seqlevels. Which annotation release will have these levels?

Signac scRNA-ATAC ensdb • 260 views
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