Dear all,
I am processing my RNA-seq data, during processing I observed multiple ensembl gene IDs for the same gene name (symbol). I went into the details and found these are from alternate loci (haplotypes/patches). Can anyone provide the complete list of genes (gene names/symbols) which are having multiple ensembl gene ids, due to haplotypes/patches for hg38 human genome build.
It would be very helpful if you can also provide your views on how genes having multiple ensembl gene ids should be treated while differential analysis by various programs. ENSEMBL gene ID from primary assembly or haplotype showing highest read counts/expression or sum of read counts/expression from all ensembl gene ids for the same gene (symbol), what should I choose to deal with such a situation in best possible ways.
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