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Old 02-05-2013, 09:08 AM   #1
Location: Barcelona

Join Date: Feb 2012
Posts: 49
Default UCSC refSeq Gene and hg19 coordinate

I have a list of mRNA NM_ numers.
In UCSC, hg19->refGene table, I can get exons and cds coordinates for every NM_.

However, when I pull out a subsequence from hg19 based on refGene coordinates, the result seems to be not correct for reverse strand. Reverse complement of the pulled exons dosn't work as well.

I have a: NM_012345.3
From UCSC i know, that for NM_012345 the first CDS is beetwen 50000:50100, strand: "-", chr1
Then I use:
samtools faidx /path/hg19.fa chr1:50000-50100
The result doesn't start with ATG (and it should starts).

Where is the problem? I know that UCSC doesn't use the version (NM_012345 instead of NM_012345.3) but it should work.

(hg19 is downloaded from
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