Hello Jianpeng,
The -X value of 1000 in Galaxy is more permissive than the Bowtie
default value of 250. If you want to modify, then using a smaller test
set of your specific data and working with the related parameters to see
if the results are what you expect would be the best approach.
Specifically - you'll probably want to look at what is kicked out as
invalid if you lower the max threshold, and determine if that is good or
bad for your experiment.
Some more help is below (also on the tool form).
You also asked me (direct):
For local galaxy, can I update the tools freely ? For example, I want to update
the Tophat. Will that work on our local galaxy if I update the Tophat ?
If you are not intending to do tool development, then using the known
dependencies is the recommendation.
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies
That said, you are certainly free to modify any part of Galaxy that you
want - tools, wrappers, and any other components are all options. Galaxy
is open source. It is just important to know that changes in tools that
deviate away from the known working version (and other dependencies)
means that there are no guarantees about functionality. The tool wrapper
and other tools that may interact with that tool (or actions, like
workflows) could continue to be functional or be fully functional. Or,
the tool could fail outright or have hidden bugs or other unpredictable
problems with that tool itself or other Galaxy components it interacts
with. These are not intractable problems - and this is exactly the
process to upgrade a tool. To make the change then find the problems and
fix them - and this is done all the time. I wanted to be clear about the
scope because this is probably much more change than most want to deal
with, unless development is the goal.
Best,
Jen
Galaxy team
---
The -X option is defined in the Bowtie manual at:
http://bowtie-bio.sourceforge.net/manual.shtml#alignment
It pairs with the -I option, both are here:
-I/--minins <int>
The minimum insert size for valid paired-end alignments. E.g. if -I 60
is specified and a paired-end alignment consists of two 20-bp alignments
in the appropriate orientation with a 20-bp gap between them, that
alignment is considered valid (as long as -X is also satisfied). A 19-bp
gap would not be valid in that case. If trimming options -3 or -5 are
also used, the -I constraint is applied with respect to the untrimmed
mates. Default: 0.
-X/--maxins <int>
The maximum insert size for valid paired-end alignments. E.g. if -X 100
is specified and a paired-end alignment consists of two 20-bp alignments
in the proper orientation with a 60-bp gap between them, that alignment
is considered valid (as long as -I is also satisfied). A 61-bp gap would
not be valid in that case. If trimming options -3 or -5 are also used,
the -X constraint is applied with respect to the untrimmed mates, not
the trimmed mates. Default: 250.
These can interact with the -3 or -5 trimming options, in the manual:
http://bowtie-bio.sourceforge.net/manual.shtml#input
Also here:
-5/--trim5 <int>
Trim <int> bases from high-quality (left) end of each read before
alignment (default: 0).
-3/--trim3 <int>
Trim <int> bases from low-quality (right) end of each read before
alignment (default: 0).
On 5/6/12 9:26 AM, Xu, Jianpeng wrote:
Hi,
I noticed that there is a parameter: Maximum insert size for valid
paired-end alignments (-X) for bowtie on Galaxy. The default value on
Galaxy is -X 1000. I was wondering if this is the default value we
should use ? Or we need to change it to another value ?
Thanks a lot.
Jianpeng
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