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Question: NCBI Genome Remapping Service- clinical remap result difference with UCSC hg19
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17 months ago
Sudhir Jadhao • 60
India

Hello Everyone

I have cDNA variant of LRG (Refseq) sequences (e.g. NM_020469.2:c.467C>T) want to convert to hg19 genomic co-ordinate. For the same I am using "NCBI Genome Remapping Service- clinical remap " online service.

Parameter selected: I have data on : LRG I want to map to:hg19

my Input;

NM_020469.2:c.467C>T
NM_020469.2:c.318C>T
NM_020469.2:c.220C>T
NM_020469.2:c.189C>T
NM_020469.2:c.188G>A
NM_020469.2:c.106G>T

output(vcf format): biostarvcf

Problem is in vcf output when I go to UCSC hg19 same genome position it shows me different basepair(136136770=> A [but the output given by clinical remap is G for same postion]) than clinical remap output .

So from the vcf output, all reference base pairs are not matching with UCSC hg19 genome base pair. for example biostarvcf2

Can anyone please tell me the reason and help to convert my cDNA LRG variant to hg19 genomic coordinate.

Thank you In advance,

Best Regards,
Sudhir

ADD COMMENTlink 17 months ago Sudhir Jadhao • 60 • updated 17 months ago RamRS 21k
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@Sudhir: it is not a good practice to create multiple questions that address similar content. Has your previous question been addressed (NCBI Genome Remapping Service- clinical remap ) satisfactorily? At first glance it seems to be what you are asking again in this question.

ADD REPLYlink 17 months ago
genomax
68k
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0

Both questions are completely different

ADD REPLYlink 16 months ago
Sudhir Jadhao
• 60
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0

No, I believe these questions are the result of the same problem. See my comment in the other thread.

ADD REPLYlink 16 months ago
finswimmer
11k
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I agree with you @fin.

I just wanted to make this question more understandable to Biostar community

ADD REPLYlink 16 months ago
Sudhir Jadhao
• 60

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