31 Mar 19:19 2015
Digest for genome <at> soe.ucsc.edu - 6 updates in 5 topics
<genome <at> soe.ucsc.edu>
2015-03-31 17:19:55 GMT
2015-03-31 17:19:55 GMT
- source of DBA2 SNPs and CNVs - 1 Update
- looking for best chains - 1 Update
- Questions about the blastz pipeline for Dmelangaster - 1 Update
- Understanding Blat Score Calculation - 2 Updates
- Track hubs button doesn't work - 1 Update
Charlotte Hor <Charlotte.Hor <at> crg.eu>: Mar 31 03:20PM
Dear UCSC Browser Team,
Is it possible to find out where the SNP, CNV etc data from the DBA2/J mouse strain come from? Is there a publication linked with these data?
Thank you for your awesome resource and best regards,
Anaïs Gouin <anais.gouin <at> irisa.fr>: Mar 31 12:08PM +0200
I would like to get the reciprocal best chains for my alignments. And I realized that your pipeline ( http://genomewiki.ucsc.edu/index.php/HowTo:_Syntenic_Net_or_Reciprocal_Best ) starts from best chains in one way (genomeA-referenced/genomeB as query).
I looked at this page http://genomewiki.ucsc.edu/index.php/Whole_genome_alignment_howto where it is said taht we have to use axtSort and axtBest to "keep only the longest chains". Is taht the way to get the best chains?
But thiese two tools are usable on axt file. So should I use it directly on the alignments on axt format or should I generate the chains with axtChain then convert the chain format in axt (if it is possible) and then use this filetring step directly on the chains?
Thanks very much in advance for your help.
"Yang, Haiwang (NIH/NIDDK) [F]" <haiwang.yang <at> nih.gov>: Mar 31 02:17AM
I contacted Ann Zweig today, and heard that the pairwise alignment between Dmel and 11 other Drosophila species will not be updated.
Therefore, I have a plan to do it myself, and here I have some questions:
I noticed in the pipeline that blastz was used, instead of the updated verion - lastz. However, the blastz is deprecated in its website.
Is the blastz really the tool that was used?
Did you used the masked genomes or unmasked genomes?
dennis <dennis <at> email.unc.edu>: Mar 29 05:33PM -0400
I have seen this question discussed but all the answers I have found
just quote the blat web page. If I have a 120 nt query and get a 28 nt
hit with 24 nt being 100% match and a 3 nt gap. Blat reports that score
as 24 but 28*2-64-x is a negative number. This is based on
2*match-mismatch-gap_penalty that is described on the web page. Can one
of you folks explain where I am making a mistake?
"Steve Heitner" <steve <at> soe.ucsc.edu>: Mar 30 12:33PM -0700
The calculation you should be using is referenced in http://genome.ucsc.edu/FAQ/FAQblat.html#blat4. The relevant portion of the script is:
my $pslScore = $sizeMul * ($matches + ( $repMatches >> 1) ) - $sizeMul * $misMatches - $qNumInsert - $tNumInsert;
The value of sizeMul is either 3 or 1 depending on whether or not your query is a protein sequence or not. Since we're not dealing with a protein sequence, the value of sizeMul is 1, so the formula is essentially:
pslScore = #matches - #misMatches - #qInserts - #tInserts
Based on what you described, it sounds like the score is roughly what it should be.
If there is still confusion, could you let us know whether you're using gfServer with hgBlat, standalone blat or something else? Also, please provide your query sequence and the name of the assembly you're querying so we can attempt to replicate your query.
Please contact us again at genome <at> soe.ucsc.edu if you have any further questions. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genome-www <at> soe.ucsc.edu.
UCSC Genome Bioinformatics Group
From: dennis [mailto:dennis <at> email.unc.edu]
Sent: Sunday, March 29, 2015 2:34 PM
To: genome <at> soe.ucsc.edu
Subject: [genome] Understanding Blat Score Calculation
I have seen this question discussed but all the answers I have found just quote the blat web page. If I have a 120 nt query and get a 28 nt hit with 24 nt being 100% match and a 3 nt gap. Blat reports that score as 24 but 28*2-64-x is a negative number. This is based on 2*match-mismatch-gap_penalty that is described on the web page. Can one of you folks explain where I am making a mistake?
"Bin Ahmad Zabidi,Muhammad Mamduh" <muhammad.zabidi <at> imp.ac.at>: Mar 30 12:34PM
It finally works! I’m using genome-euro.ucsc.edu<http://genome-euro.ucsc.edu> site since it’s a bit faster here.
On Mar 27, 2015, at 6:55 PM, Brian Lee <brianlee <at> soe.ucsc.edu<mailto:brianlee <at> soe.ucsc.edu>> wrote:
Thank you for using the UCSC Genome Browser and your question about track hubs.
Are you still seeing the error, perhaps you are visiting a mirror of the UCSC Genome Browser and not our official site, http://genome.ucsc.edu/?
Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply to genome <at> soe.ucsc.edu<mailto:genome <at> 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 genome-www <at> soe.ucsc.edu<mailto:genome-www <at> soe.ucsc.edu>.
All the best,
UCSC Genome Bioinformatics Group
On Wed, Mar 25, 2015 at 3:31 AM, Bin Ahmad Zabidi,Muhammad Mamduh <muhammad.zabidi <at> imp.ac.at<mailto:muhammad.zabidi <at> imp.ac.at>> wrote:
I’ve been trying to load my own tracks to the UCSC genome browser, but the Track hubs button doesn’t work since yesterday.
A colleague of mine here is also having the same problem.
It also doesn’t work in Chrome, Safari or Firefox on my computer.
Do you have any suggestion on how we could get around this?