Digest for genome <at> soe.ucsc.edu - 5 Messages in 5 Topics
2014-03-03 17:18:45 GMT
- quality protein sequences [1 Update]
- human-chimp alignment scores? [1 Update]
- liftover [1 Update]
- hg18 to GRCh38 through chain files [1 Update]
- problem hosting tracks on Dropbox [1 Update]
Nicholas Price <price4890 <at> gmail.com> Mar 02 04:53PM -0600
I downloaded some Tarsier protein coding sequences from the database Ensembl
and I was wondering if I could get a quality score for these so I can limit
Martin Frith <martin <at> cbrc.jp> Mar 03 05:08PM +0900
I'm trying to understand how your hg19 versus panTro4 pairwise alignments
Your documentation says you used the "human_chimp.v2" scoring matrix with
O=600 and E=150. However, this file:
Includes for example this alignment:
11 chr1 30873 30895 chr15_AACZ03171938_random 4887 4909 - 1847
The score of 1847 is correct only if you used the hoxd70 scoring matrix,
not human_chimp.v2. But I don't know if you used hoxd70 throughout your
alignment procedure, or only in later steps, or only to re-score the
alignments at the very end. Please could you clarify?
As a related question, in the same file I saw this:
##gapPenalties=axtChain O=400 E=30
##gapPenalties=blastz O=600 E=150
So were different gap scores used for axtChain, and what effect do they
have (since axtChain also has a "linearGap matrix")?
Have a nice day,
Andrei Rozanski <rozanski.andrei <at> gmail.com> Mar 03 08:29AM -0500
Im working on liftover implementation for a script.
However I was not able to find documentation about how to deal with gzip
chain files in order to get the "lifted" coordinate.
Im aware of https://genome.ucsc.edu/goldenPath/help/chain.htmlspecifications.
Any help are welcome
Centro de Oncologia Molecular
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Alexandra Vatsiou <alex.vatsiou <at> gmail.com> Mar 03 03:36PM +0100
I know that the chain file is sufficient to convert from one assembly to
another the SNP coordinates.
I have the following questions:
1. I suppose the reference sequence is the hg18 and the query is the hg38
in the hg19ToHg38.over.chain file. Right?
2. However, I can't see how exactly I will do the conversion of SNP
coordinates between the two assemblies. The chain file contains
a) the size of the ungapped alignment and
b) the difference between the end of this block and the beginning of the
next block in the reference and the query sequence.
What I have is something like the following:
SNP chr genetic dist physical dist
rs12565286 1 0.000881697 711153 C G
rs11804171 1 0.0058782819 713682 A T
rs2977670 1 0.0060252705 713754 C G
rs2977656 1 0.018904623 719811 C T
rs12138618 1 0.0633989027 740098 A G
where the fourth column is the SNP coordinates of each SNP.
For example according to the chain file what will be the coordinate of the
I will greatly appreciate if anyone knows how to deal with this.
Look forward to your reply.
Carlos Infante <cinfante <at> uga.edu> Mar 03 03:29PM
I have the same problem with bigWigs hosted on Dropbox reported by Daofeng Li<https://groups.google.com/a/soe.ucsc.edu/forum/#!searchin/genome/dropbox/genome/jytmZmvYquU/ef-OpEtUo44J> and Elphege<https://groups.google.com/a/soe.ucsc.edu/forum/#!topic/genome/P1RtZNi5pqU> After emailing back and forth with support at Dropbox, they blame UCSC web browser since they are serving the files. See the final email from Dropbox support below. Has the approach to loading custom track changed?
Begin forwarded message:
I've looked into this issue further, and it appears that the issue you're experiencing comes as a result of the 3rd party website you've been using, not with Dropbox.
From what we can tell, it's the website that's not loading the Dropbox links correctly; we're serving the files to the website, but we can't control how the website handles the files after we do so.
I'm sorry not to be able to assist you with this issue further, and please feel free to reach out with further questions!
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