[Galaxy-user] [Fwd: Re: Randomization etc.]

classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view
|

[Galaxy-user] [Fwd: Re: Randomization etc.]

Anton Nekrutenko
---------------------------- Original Message ----------------------------
Subject: Re: Randomization etc.
From:    "France Denoeud" <[hidden email]>
Date:    Wed, March 15, 2006 6:08 am
To:      "Anton Nekrutenko" <[hidden email]>
Cc:      "Dan Blankenberg" <[hidden email]>
--------------------------------------------------------------------------

Anton,
I used the randomozation tool, it seems to do exactly what I need it to
do (and is faster than my script!) : thanks!

Just two details:
- the links to the UCSC browser are not working because of the "." in
the 5th column (probably my mistake, as I put "." in the input file,
because I am more used to gff format).
- would it be possible to ask for several runs at the same time ? I
usually generate 10 (sometimes 100) random sets to calculate the random
overlap in a more robust way. Then, it would be usefull to be able to
save the outputs all at once: is it possible in Galaxy?

Two more general comments about galaxy:
- would it be difficult to make it handle gff format?
- would it be difficult to make it handle ENCODE coordinates (and add a
tool to do the encode2chr conversion if needed ?).

France.


> France,
>
> Try new randomizer at http://test.g2.bx.psu.edu written by Dan
> Blankenberg ([hidden email])
>
> It is slower, but takes strands into account and returns correct
> coordinates now. However, it not well tested yet, so be a beta-tester.
>
> anton
>
>
> Anton Nekrutenko
> Assistant Professor
> Department of Biochemistry and Molecular Biology
> Center for Comparative Genomics and Bioinformatics
> 505 Wartik Building
> PennState University
> University Park, PA 16802
> 814 865-4752
> 814 863-6699 FAX
> [hidden email]
> http://www.bx.psu.edu/~anton
> http://g2.bx.psu.edu
>
>
> On Mar 14, 2006, at 1:28 PM, France Denoeud wrote:
>
>>
>>> France,
>>>
>>> We can change the tool to take care of the strand information.   We
>>> are currently re-writing our set operation and we'll redo the
>>> randomizations as well (it uses the same underlying library).
>>> This  will take a few weeks.
>>>
>>>
>>>> More worrying, they do seem to fall inside ENCODE regions (I looked
>>>> using the "display at UCSC" link).
>>>>
>>>
>>> This is normal as the tool currently only allows you to generate
>>> regions within ENCODE. Do you want the whole genome?
>>>
>>>
>>>
>> Oops,
>> I forgot a "not" : they do NOT fall inside ENCODE regions but at  the
>> beginning of the chromosomes, like if a shifting step had been
>> forgotten...
>>
>>>> Another thing: I am trying to generate a random set mimicking a
>>>> set of
>>>> 616 objects and I get only 612 objects, is it normal ?
>>>>
>>>
>>> You have 4 regions with length 1 (not really ranges, but points):
>>>
>>> chr7    116096515    116096516    racefrag_15    .    +    1.0
>>> chr7    115906408    115906409    racefrag_13    .    +    1.0
>>> chr19    60020799    60020800    racefrag_312    .    -    1.0
>>> chr11    64079672    64079673    racefrag_561    .    +    1.0
>>>
>>>
>>>> (by the way, is it possible in galaxy to be using two different
>>>> "histories" at the same time?)
>>>>
>>>
>>> Yes:
>>>
>>> 1. Click "share history" and bookmark the link
>>> 2. Click "You may also create a new history by clicking here"
>>> 3. Get the first query in and click "share history" and bookmark
>>>
>>> Now you can simply switch between the two using bookmarks (use
>>> browser tabs)
>>>
>>> anton
>>>
>>>
>>>
>>> Anton Nekrutenko
>>> Assistant Professor
>>> Department of Biochemistry and Molecular Biology
>>> Center for Comparative Genomics and Bioinformatics
>>> 505 Wartik Building
>>> PennState University
>>> University Park, PA 16802
>>> 814 865-4752
>>> 814 863-6699 FAX
>>> [hidden email]
>>> http://www.bx.psu.edu/~anton
>>> http://g2.bx.psu.edu
>>>
>>>
>>>
>>
>
>