Question: Gene annotation help
0
gravatar for mms140130
15 days ago by
mms14013050
mms14013050 wrote:

I have downloaded gene annotation not sure from which website and I have the following data

geneName chrom txStart txEnd
A1BG    chr19       58858171 58864865
A1BG-AS1 chr19      58863335 58866549
A1CF chr10              52559168 52645435

then I looked at the UCSC website hg18 refFlat data and got the following

A1BG      chr19     63549983    63556677
A1BG-AS1    chr19   63555147    63558361
A1CF    chr10       52229174    52315441

which one to trust I have the same gene with same chromosome but different txstart and txend

Please help

Thanks

gene • 160 views
ADD COMMENTlink modified 15 days ago by Sparrow_kop90 • written 15 days ago by mms14013050
3
gravatar for Sparrow_kop
15 days ago by
Sparrow_kop90
China
Sparrow_kop90 wrote:

Hi, they are different version of genome assembly, the former is hg19 or Grch37, the latter one is hg18, so different version has different coordinate. I suggest you use hg19 or hg38, which is better than hg18, you can download from UCSC Genome or Ensembl.

ADD COMMENTlink modified 15 days ago by Emily_Ensembl13k • written 15 days ago by Sparrow_kop90

Thank you very much that really helped :)

ADD REPLYlink written 15 days ago by mms14013050
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