I am using ballgown to analyze my assembled RNAseq data, and I have noticed that the ballgown object pulls the attribute from the input gtf file called "gene_id". What is more informative for my purposes is for it to pull the "gene_name" attribute when it creates the ballgown object (sample gtf line is below):
chr1 StringTie exon 14362 14829 1000 - . gene_id "MSTRG.2"; transcript_id "rna-NR_024540.1"; exon_number "1"; gene_name "WASH7P"; ref_gene_id "gene-WASH7P";
Does anybody know how I can get it to grab the "gene_name" instead? I have played around with the getGenes function and it only pulled truncated versions of the gene name. genenames = getGenes("stringtie_merged.gtf", structure(bg_PTSD)$trans, attribute = "gene_name")
