Hello, I wanted to thank you for making this great resource accessible. We are interested in the expression of several lncRNAs. When I checked their expression in the gene_tpm_matrix_all_samples.tsv, they are shown as having an expression of zero. However, we have decided to process the data starting with the transcripts. When looking at the transcripts, I cannot find the same genes. I provide my example code in R below. The main thing I?m trying to understand is: were these genes measured and their expression is zero or were they not measured? Thank you very much in advance for your answer! Best, Anja Hartewig ``` GLASS_RNA_seq <- read.delim(paste0(input_dir, "gene_tpm_matrix_all_samples.tsv")) # one of our genes of interest is NEAT1 grep("NEAT1", GLASS_RNA_seq$Gene_symbol) # returns 29477, rowSums is 0 ``` ``` # the ENSG identifiers and transcripts were extracted from gencode v30 # I double-checked them from ensemble.org on 11.04. (GrCh38.p14) GLASS_RNA_seq_tx <- read.delim(paste0(input_dir, "transcript_count_matrix_all_samples.tsv")) ENSEMBL_transcripts_NEAT1 <- c("ENST00000501122", "ENST00000601801", "ENST00000499732", "ENST00000670617", "ENST00000645023", "ENST00000646243", "ENST00000642367", "ENST00000612303", "ENST00000616315") sum(GLASS_RNA_seq_tx$target_id %in% ENSEMBL_transcripts_NEAT1) # returns 0 ``` ``` # I also tried using EnsDb.Hsapiens.v75 library(EnsDb.Hsapiens.v75) GLASS_ensembl <- EnsDb.Hsapiens.v75 tx_to_gene_anno <- transcripts(GLASS_ensembl, return.type = "data.frame") NEAT1_anno <- tx_to_gene_anno[grep("ENSG00000245532", tx_to_gene_anno$gene_id), ] sum(GLASS_RNA_seq_tx$target_id %in% NEAT1_anno$tx_id) # also returns 0 ```