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Gene annotation help

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
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updated by Sparrow_kop Sparrow_kop • written by mms140130 mms140130

1 answer

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.

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updated by Emily Emily • written by Sparrow_kop Sparrow_kop

Thank you very much that really helped :)

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written by mms140130 mms140130

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