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wondering if motif change is needed for the gene NIPA1 in hg19 #6

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Tianyibian opened this issue Dec 12, 2023 · 1 comment
Open

wondering if motif change is needed for the gene NIPA1 in hg19 #6

Tianyibian opened this issue Dec 12, 2023 · 1 comment
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enhancement New feature or request

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@Tianyibian
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Hello, I'm reviewing the STR coordinates in the reference bed file for hg19 assembly. I noticed that the gene NIPA1 is located on the minus strand in hg19, while in the newer hg38 assembly, it's placed on the positive strand. As a result, when I examine the hg19 coordinates in a genome browser, the motif appears as CGC, contrasting with the GCG motif in hg38. I'm unsure about how TRGT functions and whether it can detect such changes.
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hg38
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@hdashnow
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Thanks @Tianyibian! We will have to think how to adjust our data format to account for these kinds of differences.
I really appreciate you taking the time to look at these loci in detail.

@hdashnow hdashnow added the enhancement New feature or request label Dec 15, 2023
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@hdashnow @Tianyibian