Hi,
I want stable Ensembl ids of genes. I have used Hyperlink Management System. In output there are some genes which have more than one Ensembl ID. I want to ask that why genes have more than one Ensembl ID and which ID should be used for further processing?
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BAGeno
2 answers
You can search for genes using gget search and then check which chromosome the IDs are on (this will tell you whether they are different haplotypes) using gget info: https://github.com/pachterlab/gget
In your example, you can see that one is on chr2 and the other on an alternate haplotype. Consequently, it makes sense for there to be two IDs.
What part of it do you not understand? I'm not going to write some multi-paragraph reply when a single sentence will suffice.
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It would help if you gave an example. In general, a "gene" is an abstract concept, which some sources (e.g., UCSC) will assign to multiple places on the genome. Such cases will result in the "same" gene having multiple IDs.
Like in case of ABCB11 there are two ensemble ids ENSG00000073734 and ENSG00000276582.