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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