I have two datasets, both from the same cell type and same genome build. One data set is chip-seq, windowed at either 1MB or 100Kb. The other is from a tiled array, with probes placed ~2-3kb apart.
I want to window the latter at either 100Kb or 1Mb (an averaging of the values will suffice), and then intersect the two data sets so that for each window I'll have two data points: the chip-seq and the tiled array values.
It seems like this should be possible using Galaxy, but I'm struggling with what the workflow should be. Does anyone have a workflow, or suggestions?
Thanks in advance,
Hi everybody, sorry for bother youwith a silly question. I have a list with a
LOT of rice loci (LOC_Os...) uploaded to Galaxy as a unique file, and would like
to obtain just the sequence of them. I tried to use the Gramene, but I couldnt.
"N" in the file "All SNPs in Personal Genomes" implies lack of information. The file has SNP data from the Southern African genomes as well as a lot of other published personal genomes. For the other personal genomes, we did not have the consensus calls at all locations (we just have the SNP locations and calls) and hence that lack of information is depicted by the base "N". For the Southern African genomes, the lack of information could be because of the method used e.g. genotyping does not give the consensus call on every location, or because we had no coverage on that location.
In the future, please send Galaxy questions / correspondence to one of the Galaxy mail lists ( galaxy-dev(a)bx.psu.edu, galaxy-user(a)bx.psu.edu, galaxy-bugs(a)bx.psu.edu ) instead of my personal email address.
On Oct 14, 2010, at 5:00 AM, Oskar Hallatschek wrote:
> Dear Greg,
> could you please let me know whether an entry "N" in the file "All SNPs in Personal Genomes" refers to an unidentifiable base,
> and why there are so many such entries in the displayed Genome.
> many thanks,
> Oskar Hallatschek
> MPI for Dynamics and Self-Organization
> Biological Physics and Evolutionary Dynamics
> Bunsenstr. 10, D 37073 Goettingen
> phone: +49-551-5176-670
> fax: +49-551-5176-669
> e-mail: oskar.hallatschek(a)ds.mpg.de
Greg Von Kuster
Galaxy Development Team
Following the discussion on this topic, the solution:
You can run R 'straight' in galaxy without a wrapper:
<command>R --slave --vanilla --file=$GALAXY_ROOT_DIR/tools/Rscript
--args $infile $outfile</command>
The input is never a big problem in galaxy, but how to capture the
output was not so clear to me. So,
Make sure your output file can be seen by galaxy (which was basically my
<param name="infile" type="data" format="tabular"/>
<data name="outfile" type="data" format="tabular"/>
And in R making sure, the output file has a name as well:
write.table(data, sep="\t", file=out.file, row.names=F)
Thanks for all the help!!
Dear galaxy team,
I would like to know whether it is possible to perform LastZ (multiple
sequence alignment tool for aligning different genomes to each other) ?
if so then how ? is there a tutorial you can refer me to ?
Bioinformatics Core Facility
National Institute for Biotechnology in the Negev
Building 51, room 314
Ben-Gurion University of the Negev
Beer-Sheva 84105, Israel
Tel: 08-6479034 054-7915931
Dear Galaxy team,
the sorter function under filters has a defect:
it only ever sorts on the c1 column
always in ascending order, alphabetical style
We tried many times with a test data file.
However, it DOES work on the main.g2.bx.psu.edu site.
So, the local galaxy-dist is the problem.
Could you please look at this and correct it?
Freddy de Bree
Hi Galaxy team:
Apologies if this is the wrong place to post this question, but is
there an API in bx-python that I can use to extract sequence out of a
Thanks for your help,
Have you seen this:
They have updated their annotation in 2010.
> Message: 2
> Date: Wed, 6 Oct 2010 09:13:09 +0200
> From: "NONELL MAZELON, LARA"<lnonell(a)imim.es>
> To: "galaxy-user(a)bx.psu.edu"<galaxy-user(a)bx.psu.edu>
> Subject: [galaxy-user] Reannotate microarray data
> Content-Type: text/plain; charset="us-ascii"
> Dear Galaxy team,
> I just discovered your tool and is fantastic!. I want to reannotate the porcine affymetrix microarray. So I wanted to perform the following steps:
> 1. Run blat/blast to the porcine genome SGSC sscrofa9.2/susScr2 with the sequences of all probes on the array (which i have in a csv file)
> 2. Get genes
> 3. Do the same with human genome
> I can load my file and the entire pig genome but i do not know how to perform the "alignment"
> Is it possible to perform blat/blast (or any other alignment tool similar) through Galaxy?
> Thanks very much in advance,
> <mailto:firstname.lastname@example.org>Lara Nonell
> Microarray Analysis Service
> Scientific and Technical Services
> IMIM-Hospital del Mar
> Barcelona Biomedical Research Park (office 166)
> Doctor Aiguader, 88 | 08003 Barcelona
> Tel.+34 933 160 577 | Fax +34 933 160 410