Hello, I need to convert a long list of FlyBase IDs into Gene Symbols. The FlyBase IDs came from a GTF file I downloaded from http://ftp.ensembl.org/pub/release-106/gtf/drosophila_melanogaster/Drosophila_melanogaster.BDGP6.32.106.gtf.gz. A short sample of the list is pasted below. I was using this tool to convert my IDs to gene symbols: https://www.biotools.fr/drosophila/fbgn_converter. This tool works great for the "FBgn" IDs, but it doesn't convert the "FBti" or the IDs that start with "RR." Does anyone know another tool that will convert the "FBti" and "RR" names?
List_Sample: FBgn0036831, FBgn0052475, FBgn0030840, FBgn0031512, FBgn0051226, FBgn0036833, FBti0018967, FBgn0267798, FBgn0265089, FBgn0030841, FBgn0003372, FBgn0043575, FBgn0002933, FBgn0035154, FBgn0034899, FBgn0035638, FBgn0031550, FBgn0033277, FBgn0038523, FBgn0266733, FBgn0266734, FBgn0003377, FBgn0031000, FBgn0038241, FBgn0054026, FBgn0051698, FBgn0039438, FBgn0003373, FBgn0003374, FBgn0034901, FBgn0004592, FBti0019012, RR51007_transposable_element, RR48341_transposable_element
Thank you for your help!!
All of the Gene Symbols for genes (i.e.,
FBgn[0-9]+) are included in a gff3:3L FlyBase gene 18917581 18919259 . + . ID=gene:FBgn0036831;Name=CG6839When you go to flybase, the annotation
Annotation Symbol CG5032forFBti0019012is present. However, for transposable element genes (i.e.,FBti[0-9]+) there is no such annotation. Are you sure transposable elements and transposable element genes are given Gene Symbols?