FeatureCounts has duplicate Gene names

Question

[Confused_human]

While doing RNA seq data analysis after mapping my featurecount data with annotation gtf file .

in almost half cases I found duplication of gene for 2 different ENSEMBLE IDs , now for downstream DESeq2 analysis how will I deal with this duplications ?

Examples of some duplications :

ENSG00000258137.6   GPR84-AS1   82  102 102 116 107 122 61  71  53  56  47  60
ENSG00000258086.1   GPR84-AS1   83  93  96  101 112 100 65  91  65  80  67  91
ENSG00000015479.20  MATR3   198 269 210 239 284 272 178 207 181 140 242 226
ENSG00000280987.4   MATR3   4   7   4   2   5   5   3   8   2   6   2   5

Answer 1

[GenoMax]

See these past answers:

Alternative sequence gene Ensembl ID
Why am I getting different ensembl gene ids for a given gene symbol?