Hello Zhang,
It looks like you may be looking at the wrong file. The snippet you
provide
below is from the file located in the hg18 directory here:
http://hgdownload.cse.ucsc.edu/goldenPath/hg18/vsMm9/axtNet/
That is, the human assembly (hg18) is listed first, and mouse (mm9) is
listed
next. I can tell this is so, because the mouse does not have 21 chromosomes.
This should explain the discrepancy you are seeing. If you look at the file
with this new information in mind and you are still not able to understand it,
please feel free to write back to the list.
Regards,
----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu
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zhuqiang zhang wrote:
> Dear sir:
> I downloaded the blastz result of mm9 vs hg18 from
> http://hgdownload.cse.ucsc.edu/goldenPath/mm9/vsHg18/axtNet/ . But I
> found the location numbers of hg seqs in those files are strange.
> For example:
>
> 3 chr21 9885041 9885155 chr12 5667727 5667849 - 771
> GGTCAAGTAACTGAGGACAAGGATCAATAGAAACAAGGACACACTCTAATTTTATGATAAATATTTTATTCAAGAGTCACCGTATACAGAAAATTCAAAG---------------ATTAGTAAAGGCCCt
> GATTAAATCATTAAGGA-AGGGAATAAAAACACTATGAACTCATTC---TCTTTTAATTGGTAATTTTCCCAA---TCGCTCTTCATGCAAGATGTAGAGTGAAGGGCCCTCTCAGTTAGTAAAGCTTTT
>
> As described, the human seq block is located at "chr12 5667727
> 5667849"; But in fact, the latter sequence is at
> "chr1:42836935-42836958". You can confirm that with Blat tools.
>
> Thank you! I appreciate your time very much!
>
> Zhuqiang, Zhang
> Institute of Zoology, CAS, Beijing
> _______________________________________________
> Genome maillist - [email protected]
> http://www.soe.ucsc.edu/mailman/listinfo/genome
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