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?
-------- Original Message --------
Subject: Re: [Genome] Chimp assembly 2 pairwise alignments
Date: Mon, 07 May 2007 16:00:42 -0700
From: Archana Thakkapallayil <archanat(a)soe.ucsc.edu>
To: Daniel Gaffney <daniel.gaffney(a)mcgill.ca>
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:
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
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.
From the expanded list, select "Extract MAF blocks". First
genomic intervals (query 2) and then press "Next Step" and
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
If you have questions about using Galaxy, you can contact their help desk:
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
UCSC genome Bioinformatics Group
Daniel Gaffney wrote:
I have ~ 1500 small regions in the human genome, for which I would like
to get the human-chimp
pairwise alignment for the latest chimp assembly. However, I'm having a
little trouble in figuring out the best
way to do this - can this be done locally? Or is there a batch
submission tool that I can retrieve all alignments
from UCSC directly - I've tried the table browser, but I can't seem to
get the specific region I want (i.e. if i select the chimp chain
track, and retrieve sequence, I get the the alignment of that entire
region, not just the region corresponding to the coordinates I've
entered). Any ideas?
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