Entering edit mode
6 months 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?