Chip-chip data
by Laura Elnitski
Hi-
the chip-chip data is in wiggle format and galaxy sends this message
error, format: wig, database: hg17
Info:
------------------------------------------------------------------------
--- Reached output limit of 100000 data values, please make region
smaller, or set a higher output line limit with the filter settings.
------------------------------------------------------------------------
---
A search for only chr 7 produces the same error as the whole genome
search. Is there any way to do a minimum of one chromosome at a time?
Thanks very much,
Laura
Laura Elnitski, Ph.D.
Head Genomic Functional Analysis Section
Genome Technology Branch
National Human Genome Research Institute
National Institutes of Health
5625 Fishers Lane, Rm. 5N-01R
Rockville, MD 20852
phone: 301-451-0265
fax: 301-435-6170
15 years, 6 months
test
by Anton Nekrutenko
test
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
anton(a)bx.psu.edu
http://www.bx.psu.edu/~anton
http://g2.bx.psu.edu
15 years, 7 months
Re: [Galaxy-user] New version of Galaxy
by Julien Lagarde
Hi Anton,
amazingly i was just about to send you the 'user account' suggestion ;-)
does that mean that when sharing a history with other people, the
history owner would be able to set basic read/write access to it? that
would be very useful!
i have another suggestion: when creating a new history item with the
left-pane tools, and then editing its attributes to make it more
human-readable, would it be possible to keep its original attributes
somewhere? for instance:
1- i subtract gencode exons from my est alignments
2- i rename the output to 'ESTs not overlapping gencode exons'
3- i do whatever operation on 'ESTs not overlapping gencode exons'.
let's say it gives me weird results, so i want to check if i did the
right thing at step 1. AFAIK this is impossible right now.
see what i mean?
cheers
j
Anton Nekrutenko wrote:
> Folks,
>
> A new version (2.2) of Galaxy is available at
>
> http://g2.bx.psu.edu:8889
>
> Aside from completely new underpinnings it now features USER ACCOUNTS
> and the ability to have MULTIPLE HISTORIES for each user.
>
> IMPORTANT -> THIS IS A TEST SITE. Once we move it to the production
> level all histories will be LOST.
>
> The stable version of Galaxy, Galaxy2ENCODE and the old test site are
> still available at the following URLs:
>
> http://main.g2.bx.psu.edu
> http://encode.g2.bx.psu.edu
> http://test.g2.bx.psu.edu
>
> SEND FEEDBACK to galaxy-user(a)bx.psu.edu
>
> ----------------------------------------------------------------------------------
>
> New to Galaxy? See these two movies:
>
> Here is a short QuickTime movie showing Galaxy's usage example:
>
> http://www.bx.psu.edu/~james/galaxy_screencasts/JoinSNPs.mov
>
> A more complex example [requiring popcorn (or beer) -> 20 min] with
> ENCODE data is here:
>
> http://www.bx.psu.edu/trac/local/encodeAnalysisExample.mov
> ----------------------------------------------------------------------------------
>
>
> Thanks for your support!
>
> Galaxy Team
>
>
> 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
> anton(a)bx.psu.edu
> http://www.bx.psu.edu/~anton
> http://g2.bx.psu.edu
>
>
>
--
----------------------------------------------
Julien Lagarde
Genome Bioinformatics Research Group
GRIB/IMIM
Pg. Maritim de la Barceloneta 37-49
E-08003 BARCELONA - Spain
Tel: +34 93 224 0886
--------------------
15 years, 7 months
Suggestion for galaxy
by anton＠bx.psu.edu
---------------------------- Original Message ----------------------------
Subject: suggestion for galaxy
From: "Julien Lagarde" <jlagarde(a)imim.es>
Date: Wed, March 15, 2006 6:56 am
To: "Anton Nekrutenko" <anton(a)bx.psu.edu>
Cc: "France Denoeud" <fdenoeud(a)imim.es>
--------------------------------------------------------------------------
Hi Anton,
here's an important feature galaxy should have, in our opinion: a
'restore deleted item' capability.
E.g. the 'delete' link available for each history item should be a 'send
to trash' instead. The user's trash should be easily accessible from the
interface , 'empty-able' by the user, and emptied by your server e.g.
every 2 days or so.
thank you!
j
--
----------------------------------------------
Julien Lagarde
Genome Bioinformatics Research Group
GRIB/IMIM
Pg. Maritim de la Barceloneta 37-49
E-08003 BARCELONA - Spain
Tel: +34 93 224 0886
--------------------
15 years, 7 months
[Fwd: Re: Randomization etc.]
by anton＠bx.psu.edu
---------------------------- Original Message ----------------------------
Subject: Re: Randomization etc.
From: "France Denoeud" <fdenoeud(a)imim.es>
Date: Wed, March 15, 2006 6:08 am
To: "Anton Nekrutenko" <anton(a)bx.psu.edu>
Cc: "Dan Blankenberg" <djb396(a)psu.edu>
--------------------------------------------------------------------------
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 (djb396(a)bx.psu.edu)
>
> 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
> anton(a)bx.psu.edu
> 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
>>> anton(a)bx.psu.edu
>>> http://www.bx.psu.edu/~anton
>>> http://g2.bx.psu.edu
>>>
>>>
>>>
>>
>
>
15 years, 7 months
Error with ENCODEdb
by Prachi Shah
ENCODEdb queries don't work well. Here's the error message generated:
error, format: interval, database: hg16
Info: 'module' object has no attribute 'BASEURL'
Thanks,
Prachi
15 years, 7 months
galaxy
by Laura Elnitski
Can galaxy put header lines between samples when returning genomic
DNA? Other servers want to see the separation of sequences in FASTA
files.
Thanks,
Laura
Laura Elnitski, Ph.D.
Head Genomic Functional Analysis Section
Genome Technology Branch
National Human Genome Research Institute
National Institutes of Health
5625 Fishers Lane, Rm. 5N-01R
Rockville, MD 20852
phone: 301-451-0265
fax: 301-435-6170
15 years, 7 months
