Hi Dear All, When I did RNA-Seq analysis, the GTF file I used was from NCBI. The output of cuffdiff replaced the Gene symbol (official gene symbol) with XLOC's such as:
LOC110534079 LOC110534540 LOC110537830 LOC110485322 LOC110487655 LOC110491675 LOC110492686 LOC110498361 LOC110500236 LOC110502506
LOC110537830 (ID) = mknk1 (Gene symbol)
Is there any way to convert XLOCs back to Gene symbols?
I searched repeatedly in section Gene in NCBI, but the results Were obtained as LOCs.
I also tried the following sites but it was not successful:
I also read all the relevant biostars content but did not get the required result: https://www.biostars.org/p/129299/
I also tried the following command in the R software cummeRbund package, but the output answers were as LOCs ID.
cuff <- readCufflinks() #Retrive significant gene IDs (XLOC) with a pre-specified alpha diffGeneIDs <- getSig(cuff,level="genes",alpha=0.05) #Use returned identifiers to create a CuffGeneSet object with all relevant info for given genes diffGenes<-getGenes(cuff,diffGeneIDs) #gene_short_name values (and corresponding XLOC_* values) can be retrieved from the CuffGeneSet by using: names<-featureNames(diffGenes) row.names(names)=names$tracking_id diffGenesNames<-as.matrix(names) diffGenesNames<-diffGenesNames[,-1] # get the data for the significant genes diffGenesData<-diffData(diffGenes) row.names(diffGenesData)=diffGenesData$gene_id diffGenesData<-diffGenesData[,-1] # merge the two matrices by row names diffGenesOutput<-merge(diffGenesNames,diffGenesData,by="row.names")
Does anyone have a solution to this problem? Regards