How to add annotation information to a plant genome in the treatment of single-cell ATAC with Signac？

I tried to use Signac to process plant single-cell ATAC data, but I encountered problems when adding gene annotation information to the Seurat object. Here is my code.

gtf <- rtracklayer::import("F:\\scATAC_scSeq\\Arabidopsis_thaliana.TAIR10.50.gtf")

gene.coords <- gtf[gtf$type == 'gene']

seqlevelsStyle(gene.coords) <- 'Ensembl'

gene.coords <- keepStandardChromosomes(gene.coords,pruning.mode = 'coarse')

Annotation(ATAC1) <- gene.coords

ATAC1 <- NucleosomeSignal(object = ATAC1)

ATAC1 <- TSSEnrichment(object = ATAC1,fast = FALSE)

enter image description here

annotation signac plant

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written 5.3 years ago by qzLi0031 •

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