Howdy, Uwe,
(I don't speak for the galaxy group, but I watch the list for lastz-
related messages.)
Is it possible to specify more arguments in "Full parameter list"-
mode, particularly those that're implicitely described in YASRA-mode
(match/mismatch rewards and step-size (Z/step))?
As you indicate, the galaxy wrapper for lastz only provides access to
certain combinations of arguments. At present, the only ways I know
that you would be able to access other lastz parameters would be
either to (1) write your own custom galaxy wrapper or (2) install
lastz and run it from the command line.
Kelly Vincent is planning to update the galaxy wrapper some time this
summer, so this is something she's likely to address with that update.
However, heading to "Full parameter list"-mode leads to excessive
CPU-use, because (presumably) the step-size (default=1?) is left
unset.
You are correct that the default step is 1. (defaults are shown at
the bottom of each command section in the lastz readme file which can
be found at www.bx.psu.edu/~rsharris/lastz or at the Miller Lab
website) Depending on your data, a step of 1 may be overly sensitive
causing lastz to spend a more time than necessary.
Also, it'd be great to be able to alter not only gap penalties, but
match/mismatch rewards as well. (Obviously a mismatch would cause
the same problem).
Ideally I think the wrapper interface should allow you to point at a
lastz scoring file, which can contain all the scoring parameters.
This is an oversight-- the thinking when the wrapper was written was
that the yasra settings would be sufficient (and work well) and would
simplify the user's choices, making it more likely that the user would
choose settings appropriate for their data.
I've discussed this with Kelly some, this morning. It's not clear
whether the wrapper would be better if it allowed each scoring option
to be set as a separate field, or if they were incorporated in a file,
or if (somehow) they were one of your galaxy history items. Do you
have any thoughts on that?
I'm dealing with 454 reads and it's crucial to the scenario to have
the 5' ends aligned properly (in terms of sensitivity), so all the
YASRA-templates comprising heavy gap penalties perform fairly poor
as soon as there's a gap nearby the 5' end.
The idea behind having such severe gap penalties is that 454 often
incorrectly calls the length of homopolymer runs, introducing what
will look like short gaps. As used within yasra (an assembler from
the Miller Lab, not in galaxy) these settings are probably
appropriate. But this is not an ideal general solution because it can
keep us from discovering true gaps. A better solution would probably
be to have less-severe gap penalties, with an additional context-
related gap penalty (or reward) for gaps at homopolymer runs.
However, it would be costly to add this to the alignment core inside
lastz.
The problem with gaps or mismatches close to the end of a read is
discussed in the lastz readme file, in the section "Y-drop Mismatch
Shadow". The situation can can be improved by using the --noytrim
option. This option was added to lastz after the wrapper was written,
and so is not currently available from galaxy. --noytrim tells lastz
to accept a lower-than-maximal-scoring alignment if it can reach the
end of the read. I intend to add that into the yasra settings, but
changing those raises an issue of backward compatibility that I need
to resolve.
I hope that helps. Please post a reply if I've left something
unanswered or if you have other thoughts on this.
Bob H
On Jun 6, 2011, at 6:47 AM, Appelt, Uwe wrote:
Hi @All,
short version:
Is it possible to specify more arguments in "Full parameter list"-
mode, particularly those that're implicitely described in YASRA-mode
(match/mismatch rewards and step-size (Z/step))?
long version:
I'm dealing with 454 reads and it's crucial to the scenario to have
the 5' ends aligned properly (in terms of sensitivity), so all the
YASRA-templates comprising heavy gap penalties perform fairly poor
as soon as there's a gap nearby the 5' end. However, heading to
"Full parameter list"-mode leads to excessive CPU-use, because
(presumably) the step-size (default=1?) is left unset. Also, it'd be
great to be able to alter not only gap penalties, but match/mismatch
rewards as well. (Obviously a mismatch would cause the same problem).
Examples:
AAAAAAAAAA (target)
AAAAATAAAA (query)
=> I need the alignment boundary to be found at position 1, rather
than behind the mismatched T and this cleary doesn't work as long as
the mismatch penalty is too large (same applies for gap-open/extend
penalties).
Thanks in advance and Cheers,
Uwe
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___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
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