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5.6 years ago
Leonida Monaco
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20
I had 3 dataset of SNPs. 2of them validated with hg18 and one with hg 19. I validate the hg 19 back to hg18, but 20.000 SNPs are set NT. How can I validate them manually, using R if possible?
Hello,
what do you mean by "validating"?
fin swimmer
Hi, when I converted SNPs from hg 19 to hg18, there where many thousands of them are set NT in the hg 18 database. Is there any system not to lose those NT snps? I was looking for a method that can help me in avoiding their lost other than adding them manually one by one.
If there is any.
Hello Leonida Monaco ,
please use the
ADD REPLYbutton below a post you want to reply to.I guess with "converting" you mean to get the genomic position in another reference genome? You will never be able to convert all positions from one assembly to another due to the changes that where made in the reference genomes. Some regions where added, some were deleted other are moved to another position, and so on.
Why do you need to convert from an old assembly (hg19 is outdated since 2013) to a very old (hg18 is outdated since 2009) one?
fin swimmer
Thank you for your answer.
I am a MSc student who is doing the thesis in Bioinformatics. I do what my prof tells me to do. I know that it is outdated but that's what I've been told to do.
Ok thank you by the way. I was thinking the same, but better to ask someone here in Biostars.
Thank you Sir