Hi there,
I am about to conducting GO analysis on Brassica napus in R. Since what I have so far are gene alias names (GSBRNA2Txxxxxx) and I have to convert them into corresponding official gene names/IDs (e.g. BnaC09gxxxxxx) before importing into GO analysis. To this end, I created a TXDB object via 'GenomicFeatures' package from GFF file downloaded from Genoscope (Brassica_napus.annotation_v5.gff3) and was going to retrieve gene IDs using alias names. However, I check the content of all columns in TXDB object and there was no alias names included, whilst I could see this part of info when I 'less' the GFF file in terminal.
chrC09 GazeA2 mRNA 9318184 9322857 214.6819 - . ID=BnaC09g12820D;Name=BnaC09g12820D;Alias=GSBRNA2T00000001001 chrC09 GazeA2 CDS 9322739 9322857 23.0574 - 0 Parent=BnaC09g12820D;Name=BnaC09g12820D;Alias=GSBRNA2T00000001001 chrC09 GazeA2 CDS 9322374 9322646 15.0804 - 2 Parent=BnaC09g12820D;Name=BnaC09g12820D;Alias=GSBRNA2T00000001001 chrC09 GazeA2 CDS 9320216 9320312 11.1000 - 2 Parent=BnaC09g12820D;Name=BnaC09g12820D;Alias=GSBRNA2T00000001001 chrC09 GazeA2 CDS 9320054 9320125 11.1000 - 0 Parent=BnaC09g12820D;Name=BnaC09g12820D;Alias=GSBRNA2T00000001001 chrC09 GazeA2 CDS 9319184 9319951 24.0756 - 0 Parent=BnaC09g12820D;Name=BnaC09g12820D;Alias=GSBRNA2T00000001001 chrC09 GazeA2 CDS 9318522 9318938 20.8419 - 0 Parent=BnaC09g12820D;Name=BnaC09g12820D;Alias=GSBRNA2T00000001001 chrC09 GazeA2 CDS 9318354 9318425 24.8240 - 0 Parent=BnaC09g12820D;Name=BnaC09g12820D;Alias=GSBRNA2T00000001001 chrC09 GazeA2 UTR 9318184 9318353 1.5570 - . Parent=BnaC09g12820D;Name=BnaC09g12820D;Alias=GSBRNA2T00000001001
what should I do next, should I change package for the conversion or I can simply change the code for TXDB object establishment to include the 'gene alias names' into the dataset?
Appreciate any advices:)
