TobiTekath
commented
3 months ago Hi @vasikara17, thank you for using DTUrtle and reaching out.
Just so that I understand your issue correctly: You have an Seurat object containing the gene-level expression levels, correct?
Then you can use DTUrtle to add the transcript-level expression data to the Seurat same object (as new assay dtutx by default).
I assume you have created some transcript-level quantification data (e.g. with Alevin or Bustools) - then please import this data (preferably with import_counts() and then supply the output from this function as tx_list.
See here and here for an example.
Hope this clarifies your question.
Describe the bug Hello, thanks a lot for the very useful tool. I am trying it for the first time and I am starting from the already analyzed Seurat object. I am importing and transforming the gtf file for the annotation with: tx2gene <- import_gtf(gtf_file = "Mus_musculus.GRCm39.109.gtf.gz") tx2gene$gene_name <- one_to_one_mapping(name = tx2gene$gene_name, id = tx2gene$gene_id) tx2gene$transcript_name <- one_to_one_mapping(name = tx2gene$transcript_name, id = tx2gene$transcript_id) tx2gene <- move_columns_to_front(df = tx2gene, columns = c("transcript_name", "gene_name"))
Then I run: cts<-seur_obj_sub@assays$RNA$counts
seur_obj_sub <- combine_to_matrix(tx_list = cts ,seurat_obj = seur_obj_sub, tx2gene = tx2gene) **since I have a Seurat object what is the tx_list input I schould use?
Error: Trying to infer cell extensions from Seurat object Error in combine_to_matrix(tx_list = cts, seurat_obj = seur_obj_sub, tx2gene = tx2gene) : Could not 1:1 map inferred seurat cellname extensions and tx file list. Either provide explicit cell extensions or try subsetting the seurat object, if you do not want to provide tx information for all samples.
Thank you in advance for yout time!