Question: [Fwd: Re: [Genome] Chimp Assembly 2 Pairwise Alignments]
0
Daniel Gaffney • 10 wrote:
Hi there,
further to the query below, I'm trying to follow the steps outlined in
the email below to send the
28way genome alignment to galaxy. I'm currently waiting on this job to
complete on galaxy - as mentioned
below, it does take some time, but can anybody give me an idea of how
long this might take (its already been running for
a while)? Is it likely to be minutes/hours/days?
Cheers
Dan
Subject: Re: [Genome] Chimp assembly 2 pairwise alignments
Date: Mon, 07 May 2007 16:00:42 -0700
Reply-To: archanat@soe.ucsc.edu
To: Daniel Gaffney <daniel.gaffney@mcgill.ca>
CC: genome@soe.ucsc.edu
References: <463F58BC.8050306@mcgill.ca>
Hello Dan,
Here is the response from one of our engineers:
I think that the easiest way to do this is using Galaxy 2. This method
will involve using the pairwise alignments extracted from the multiz
multiple alignment (from the Conservation track). This is a best in
genome alignment with the best aligning region for chimp aligned to
each
region of the human genome. This means that there is less information
than in the chain track which contains all alignments (passing certain
criteria) of the chimp genome to each region of the human genome. If
this is ok, then you can use Galaxy by going to:
http://test.g2.bx.psu.edu/
You will need to use the test version of Galaxy because this has the
option of using our genome-test server. There are only panTro1
alignments in the 17-way alignment on hg18, but there are panTro2
alignments in the 28-way on hg18. Be aware that this our test server
and
that some of the data here (including the 28-way alignment) has not
gone
through our rigorous quality assurance checks.
Here are the instructions to follow:
1) Go to http://test.g2.bx.psu.edu/
2) Click on "Get Data" in the pane at the left side.
3) Click on "UCSC Test table browser" link in the expanded list.
4) In the middle an interface will appear that looks like the Table
Browser. You can then select the Human Mar 2006 (hg18) assembly.
Select
Comparative Genomics as the group, 28-way Cons as the track and
"multiz28wayAnno" as the table. Make sure that genome is selected as
the
region. Then select MAF as the output type.
5) Check the box that says "Send output to Galaxy". Press "get output"
button and the "Send query to Galaxy" button. (Up to this point can
also
be done in the Table Browser on genome-test). Getting the MAF output
seems to be rather slow.
6) Then from the "Get Data" menu, select "Upload File" and you can
paste
in or upload a file of the regions for which you want alignments
(position or BED format is fine).
7) Then click on the "Fetch Sequences and Alignments" in the left
pane.
genomic intervals (query 2) and then press "Next Step" and select the
MAF format output (query 1). The result is the multiple alignments for
the regions defined by the user.
8) To limit this to only the pairwise alignment between human and
chimp,
select the "Maf Limit to Species" from the left pane and choose hg18
and
panTro2.
If you have questions about using Galaxy, you can contact their help
desk:
galaxy-user@bx.psu.edu
If you would rather use the human/chimp chain or net alignments to get
alignments for specific regions of the human genome, then we can walk
you through using several of the programs that we have available for
command line use in order to extract human/chimp pairwise alignments
from this data.
I hope this information is helpful to you. Let us know if you have
further questions.
Regards,
Archana
UCSC genome Bioinformatics Group
--
================================================================
Daniel Gaffney
McGill University and Genome Quebec Innovation Centre
740 ave Dr Penfield Rm 7208
Montreal (Quebec)
H3A 1A4
http://dutch.cap.ed.ac.uk/
Tel: +1 514 398 3311 ext: 04592
Fax: +1 514 398 1790
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modified 11.6 years ago
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James Taylor • 320
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written
11.6 years ago by
Daniel Gaffney • 10
