I was looking at the gene coordinates of LDLR for the hg19 assenbly and NG RefSeq in order to convert them to each other, while I do understand the length of the gene may be different in the two assemblies, I fail to understand why should there be a difference in the length of the same gene in the two assemblies.
I do appreciate if someone can clarify it to me.
Hi Reza,
When you look over any region of your interest, you may come across some regions consisting of tandem Ns (any nucleotide) located in intergenic sequences (sometimes in long introns), which is referred to as "incomplete genomic region" (RefSeq category: NG). It means that sequence information about the regions are still being updated in order to fill in blanks (the Ns) and do some corrections. As the browsers are updated, we can see some kind of changes in terms of position or length of genes. If you have concerns about the length of the whole gene (you may need it for genotyping) or distance to any locus (such as enhancers etc), I would suggest you to use the most updated versions of GBs.
But additionally, this is the main reason why we can not operate hg19-based NGS data in hg38 or older ones. Sequences can not be aligned in any region between these versions of same browser during NGS data analysis.
Best,
Volkan
Thanks Volkan for the informative explanation!
Actually I am going to convert coordinates from RefSeqGene NG to Hg19 genome assembly and vice versa through developing an App, but, there is a problem with variable gene lengths in hg19 and NG. Do you know any tool able to handle it?!
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