liftOver , chimp genome

[可可]

Hi，

I am trying to use liftOver to convert genome coordinates between panTro2 and panTro3. I found that some different locations in panTro2 are mapped to the same location in panTro3. Still, Some locations in panTro2 are mapped to different chromosomes in panTro3. For example, chr1:842163-842168 in pantro2 is mapped to chr7:159384166-159343171 in pantro3. This is really a big change.  Are these normal? If so, what's the reason  behind it?  

Best regards,

Sha He

[Christopher Lee]

Hi Sha,

Thank you for your question about liftOver from panTro2 to panTro3. The position you reference, chr1:842163-842168, is only a 6bp region near the end (200bp) of a contig in the panTro2 assembly. A 6bp sequence is not very specific and can map to many different positions in the genome, so it is not surprising to see that the position was lifted to a different chromosome.

However, when I try to lift the sequence using default parameters on the web-based liftOver:
http://genome.ucsc.edu/cgi-bin/hgLiftOver

the sequence fails to lift because the region is partially deleted in the panTro3 assembly. If I lower the percentage of bases that must map, I'm able to map the sequence to panTro3 chr7:159384167-159384171, and not the position chr7:159384166-159343171 that you indicate. How were you running liftOver in order to get the result you mention?

For better results, you should consider lifting larger regions, such as the positions of the entire contig that chr1:842163-842168 falls on. Or blatting some sequence from the contig to the panTro3 assembly to see if the same contig was carried over between assemblies, and then finding your sequence there.

In this case, I grabbed the sequence of the contig in panTro2 that your region falls in, Contig993.46, position chr1:841,971-850,380, and blatted it to the panTro3 assembly. I've pasted the top 5 results below:

   ACTIONS      QUERY           SCORE START  END QSIZE IDENTITY CHRO STRAND  START    END      SPAN
---------------------------------------------------------------------------------------------------
browser details YourSeq         8264     1  8410  8410  99.3%     7   +  159383973 159392479   8507
browser details YourSeq         7600   811  8410  8410 100.0%     1   +     841778    849377   7600
browser details YourSeq         6901  1181  8410  8410  98.1%  Un_GL393504   +          1     10474  10474
browser details YourSeq         5733     1  8410  8410  97.4%  1_GL389243_random   +       7391     15381   7991
browser details YourSeq         1758  1374  8410  8410  96.9%  Un_GL393504   +        399      7908   7510

If you click the 2nd details link after performing the blat search, you can see that the position you are interested in (200bp from end of the contig), falls in the 800 or so bases of the contig that does not align to panTro3 chr1 (denoted by black bases instead of the aligning blue bases).

Thus for the position you've noted, it is not particularly out of place for regions to lift to different chromosomes.

Please let us know if you have any further questions!

Thank you again for your inquiry and using the UCSC Genome Browser. If
you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a
publicly-accessible forum. If your question includes sensitive data,
you may send it instead to genom...@soe.ucsc.edu.

Christopher Lee
UCSC Genomics Institute

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