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.

See Aliases of drosophila gene names.