Annotating DEXseq outputs

Hi All,

I am trying to annotate to get gene symbols,from the outputs of DEXseq results that has Ensembl gene ids in the following pattern

geneinfo_trans$gene_id
ENSG00000156011.16+ENSG00000244018.1
ENSG00000197971.14+ENSG00000279811.1
ENSG00000197971.14+ENSG00000279811.1
ENSG00000197971.14+ENSG00000279811.1
ENSG00000109971.13+ENSG00000202252.1+ENSG00000207118.1
ENSG00000167526.13+ENSG00000200084.1

I tried Biomart in R

annot<-getBM(c("ensembl_gene_id_version","ensembl_gene_id", "hgnc_symbol", "chromosome_name", "strand", "start_position", "end_position","gene_biotype"),values= geneinfo_trans$gene_id, mart=ensembl)

But it doesnt work.

I also tried using the GTF file for getting the gene symbols, like here What is the best way to match gene id with gene name. , still the same. Any help is greatly appreciated !! Thank you!!

rna-seq

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updated 6.7 years ago by Kevin Blighe

• written 6.7 years ago by gayatri281 •

You posted this a Tool, which is a tag reserved for the reporting of new tools / programs. I have changed your post to a Question, and also formatted your code and output via the 101 010 button. Please be careful the next time.

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written 6.7 years ago by Kevin Blighe

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