Hello, I am using "featureCounts" in Rsubread package for analyzing bulk RNA-seq of drosophila. Since there is no inbuilt annotations of drosophila, I am using a gtf file in the homepage of iGenomes. (Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.gtf.)
I made bam files using Rsubread referring to dm6, then I tried to use the following codes.
library(Rsubread) library(limma) library(edgeR) targets <- readTargets("wholeflyseq.txt") fc <- featureCounts(files=targets$OutputFile,annot.ext="genes.gtf",isGTFAnnotationFile=TRUE, isPairedEnd=TRUE)
I was able to obtain a file with gene symbol but is there any way to get a file with gene ID of NCBI? When I tried to convert the information of gene symbol to gene ID after I get the file, around 20% of the information was lost.
I would appreciate it if someone could inform me of how to get a file with gene ID instead of gene symbol.