KaetheKong
commented
2 years ago Hello,
I have just uploaded the gene_info.tsv into the Capybara/examples folder. Please find it there and let us know if that is helpful! It is basically a tab-delimited file with Ensembl id and the corresponding gene symbols.
For the human cell atlas, one of the resources coming from the same lab that created MCA is the Human Cell Landscape (HCL). This could be a good place to start with and I think there are many other human cell atlases that could be useful!
Hope this is helpful! Wenjun
Danyi-ZHENG
`# Use Ensembl to extract gene length information based on Ensembl ID library(biomaRt) gene.info <- read.table("gene_info.tsv", header=T, stringsAsFactors=F)
mart <- useMart("ensembl",dataset="mmusculus_gene_ensembl") ensembl.gene <- gene.info$gene.ensembl[which(!is.na(gene.info$gene.ensembl))] ensembl.map.rslt <- getBM(attributes = c("mgi_symbol", "start_position", "end_position", "ensembl_gene_id_version", "external_gene_name", "ensembl_gene_id"), filters = "ensembl_gene_id", values = ensembl.gene, mart = mart) ensembl.map.rslt <- unique(ensembl.map.rslt[,c(2:6)]) rownames(ensembl.map.rslt) <- ensembl.map.rslt$ensembl_gene_id
Calculate length of the gene
ensembl.map.rslt$gene.length <- abs(ensembl.map.rslt$end_position - ensembl.map.rslt$start_position)/1000
gene.info$gene.length <- ensembl.map.rslt[gene.info$gene.ensembl, "gene.length"]
gene.info.sub <- gene.info[which(!is.na(gene.info$gene.length)), ] rownames(gene.info.sub) <- gene.info.sub$gene.sym `
Hi! May I get to know what is this gene_info tsv? I am trying to create a human bulk reference with the file "https://s3.amazonaws.com/mssm-seq-matrix/human_matrix_v11.h5", and stuck at the above step. Btw, for a high-resolution reference, is there a human version of cell atlas recommeneded? Thank you!