Total No of Genes of GENCODE Release 43

Question

[ahmad]

Hi everyone

This is the my first post and currently am learning Bioconductor

Does anyone know why there is a different between total number of genes for GENCODE Release 43 which is 62703 (https://www.gencodegenes.org/human/stats_43.html) and number of genes once extracted using Bioconductor as the following code

gtf_43<-rtracklayer::import('gencode.v43.primary_assembly.annotation.gtf') 
dtgtf_44<-data.frame(gtf_43)
genes <- unique(obj_43[ ,c("gene_id","gene_name")]) 
nrow(genes)

The result is 62757

Thank you in advance

[ATpoint]

obj_43 is not defined in this code chunk which decreases my confidence in the result. Just count the unique gene IDs.

[ahmad]

Hello, thanks for replying, by mistake I paste the wrong code. the following is the corrected

gtf_43<-rtracklayer::import('gencode.v43.primary_assembly.annotation.gtf') dtgtf_43<-data.frame(gtf_43) genes <- unique(dtgtf_43[ ,c("gene_id","gene_name")]) geneId <- unique(dtgtf_43[ ,c("gene_id")]) length(geneId) ## result 62757 nrow(genes) ## result

[ahmad]

The following is the correct code

gtf_43<-rtracklayer::import('gencode.v43.primary_assembly.annotation.gtf') dtgtf_43<-data.frame(gtf_43) nrow(dtgtf_43) genes <- unique(dtgtf_43[ ,c("gene_id","gene_name")]) geneId <- unique(dtgtf_43[ ,c("gene_id")]) length(geneId) nrow(genes)

Answer 1

[ATpoint]

As I said, I assume that you are doing something on old/overwritten variables or a wrong GTF. This is how it is:

a<-rtracklayer::import("https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_43/gencode.v43.annotation.gtf.gz")
length(unique(a$gene_id))
[1] 62703

nrow(data.frame(a[a$type=="gene",]))
[1] 62703

[ahmad]

Thank you, its correct. In my code I was using (https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_43/gencode.v43.primary_assembly.annotation.gtf.gz) not ("https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_43/gencode.v43.annotation.gtf.gz")

Based on what I red that gencode.vX.primary_assembly.annotation contains Gene annotation on reference chromosomes and scaffolds, and gencode.vX.annotation contains annotation (genes, transcripts, exons, start_codon, stop_codon, UTRs, CDS) on the reference chromosomes. what does it mean ?and what is the different? and which one shall be use for alignment process?? Thanks in advance