Hi Arthur,
You are not seeing chain ID 439388 (listed at chr2:192280692-192283466)
in the browser at those coordinates because it is on the negative
strand. Note that in chain files (from:
http://genome.ucsc.edu/goldenPath/help/chain.html), " when the strand
value is "-", position coordinates are listed in terms of the
reverse-complemented sequence."
To get the "browser coordinates" (+) from the file (where RC=reverse
compliment):
StartRC = qSize - qEnd
EndRC = qSize - qStart
So for the chain in question:
chain 63452 chr2 242951149 + 50667683 50670457 chr2 242951149 - 192280692
192283466 439388
You would find it here in the browser:
chr2:50,667,684-50,670,457
Please let us know if you have any additional questions: [email protected]
-
Greg Roe
UCSC Genome Bioinformatics Group
On 10/31/11 12:45 AM, arthur zhou wrote:
> dear Sir,
> I have a problem on the UCSC human genome data about self-chain.
>
> I download the data: hg18.hg18.net.gz, hg18.hg18.all.chain.gz,
> &chr#.hg18.hg18.net.axt.gz
> through http://hgdownload.cse.ucsc.edu/goldenPath/hg18/vsSelf/.
>
> Then I found a position: chr2:50667684-50670457 in the UCSC Genome
> Browser. Its self alignment is itself.
>
> Then when I check it in the data downloaded, in hg18.hg18.all.chain.gz I
> just found a position chr2:192280692-192283466, which it said they are a
> couple of self-chain.
>
> But i was surprised to find that I put the
> position chr2:192280692-192283466 into UCSC Genome Browser, there was no
> self-chain displayed.
>
> Did I download wrong data sets, or maybe there is a updated one needed?
>
> I appreciate your reply soon.
>
> your sincerely
>
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