tools: merge regions of a single query
by Erika
Hi,
I've tried using the "Operate on Genomic Intervals" tool called
"Merge regions of a single query" with some puzzling results. So
from the example provided with the tool it seems that if regions fail
to merge (i.e. they are unique) then they should be returned in the
output along with the merged results, correct? I have used 3
different data files, for human hg18, chimp panTro2, and macaque
rheMac2, and each of these files has returned an empty output
result. However, they have successfully completed the operation (no
error messages were returned). Does this indicate that all regions
are unique? Does this indicate a problem with the input file? Does
this indicate a problem with the tool?
I have attached an example file.
Thank you for your help,
Erika

**********************************************************
E.M. Kvikstad
Academic Computing Fellow
IGDP Genetics
Center for Comparative Genomics and Bioinformatics
The Pennsylvania State University
208 Mueller Lab
University Park, PA 16802
(814) 863-2185
kvik(a)bx.psu.edu
15 years
edit attributes is not saving changes
by Erika
Hi,
I'm trying to use the "edit attributes" function and the server is
returning a notice indicating "attributes changed" however the
attributes changes are not actually being saved. i am specifying a
file as "genomic intervals" and i input the columns indicating
chromosome, start, end, strand. it's a simple file with only 10 lines.
thanks for the help!
**********************************************************
E.M. Kvikstad
Academic Computing Fellow
IGDP Genetics
Center for Comparative Genomics and Bioinformatics
The Pennsylvania State University
208 Mueller Lab
University Park, PA 16802
(814) 863-2185
kvik(a)bx.psu.edu
15 years
No reaction clicking any tools using internet explorer
by Taschner, P. (HKG)
Using Internet Explorer 6.0, I was unable to select any of the Galaxy
tools, although Javascript has been enabled. Clicking on any tools
results in the message Error on page. Galaxy tools seem to work using
Firefox, so you might wish to include this information on your wiki
page.
Best regards,
Peter
Dr. Peter E.M. Taschner
Department of Human Genetics
Center for Human and Clinical Genetics
Leiden University Medical Center
Postal zone: S-4-P
P.O. Box 9600
2300 RC Leiden
The Netherlands
Telephone: +31 71 5269424
Fax: +31 71 5268285
E-mail: P.Taschner(a)lumc.nl
Visiting address:
Building 2, room R04-005, Einthovenweg 20, Leiden
15 years
critical feedback
by Ross Hardison
This student was more adventurous. I think he actually could do more
of what he tried with more experience (if he wants to get GNF data he
should use that table), but there is some good feedback.
I do agree with one comment - that we should mask out buttons that
don't work on the Table Browser proxy.
"My goal is to use Galaxy to retrieve gene expression data from GNF
human gene expression atlas from UCSC genome table browser. If
possible, I will do a gene co-expression analysis for a group of
genes that are annotated as G-protein coupled receptors (GPCRs).
The first problem I met was that I could not find a place in UCSC
genome table browser to retrieve genes with annotations. I think it
is reasonable for a biologist to ask questions like: what are the
annotated G-protein-coupled receptors or MAP kinases in the human
genome. I went though a number of table schema of UCSC genome table
browser, there are no annotation in those tables. The lack of gene-
annotations in the UCSC table browser may reflect the scope of UCSC
designers and is not related to Galaxy, so I will not further discuss
this issue. I went to the GNF atlas official website downloaded
annotated probe file, and extracted all the genes annotated as G
protein coupled receptors. There are totally 385 such annotated
probesets in the public available annotation file (by custom Python
code search for annotated as “coupled” and “receptor”). I thought it
may be possible to do this operation in Galaxy, but I found in the
“Filter, sort, join and compare: Select” tool, there is no
combinatorial pattern search. It would be helpful to add a place
where people with more expertise can customize their query commands
and save them. In another word, if people already know a little about
PERL or Python, it may be desirable for them to put a short query in
those programming languages.
After obtaining the list of GPCRs, I was trying to use Galaxy to
retrieve data from UCSC table browser. I clicked on GET DATA à UCSC
main à Execute, which brought up a proxy page in the middle panel of
Galaxy interface. I found at least three functions on this proxy did
not work properly. First, the button of “describe table schema” did
not work. Second, when I clicked on “upload list”, an uploading
interface appeared in the middle panel. When I clicked “submit” after
I specified the file name, the middle panel showed “This is a proxy
to the data services provided by the UCSC Genome Browser's Table
Browser.”. and no data were received by Galaxy. Third problem was
when I specified a file name as output file in the “output file:
(leave blank to keep output in browser)”, I could not get the output
file anywhere. Clearly there are some “mis-communication” between
Galaxy and UCSC browser. It may be useful to “mask” these functions
in Galaxy to avoid frustration. What I finally did was to “PASTE
LIST” of all the probe names I got and retrieve the data from UCSC
browser. The resulted file in Galaxy is the same as what I downloaded
directly from UCSC browser website use the same set of 385 probesets
names. Totally 405 expression data were extracted from the UCSC table
browser.
The gene expression data was in the column 16 of the output file. I
did “cut columns from a table” then “Remove beginning of a file” and
then “convert delimiters to tab”. These operations gave me a file
with table delimited expression data of 405 probesets(genes). I found
that in the data browsers of Galaxy, the maximum number of columns is
27, above that, there was no straight forward way of finding out how
many columns were in the data file. Although there is a statistical
tool in the Galaxy, we can only calculate “correlation for numeric
COLUMNS”. And there is no way to transpose the data matrix.
Therefore, I could not find a way to finish my goal completely in
Galaxy.
I have learned one important lesson from the experience of using
Galaxy: the diversity of GENOMICS data is a great challenge for
people working on genomic research and for any software. Clearly,
Galaxy is a sequence-analysis centric environment. I am sure Galaxy
can do a great job in sequence analysis. However, when we are looking
for other type of genomics data, for example, gene expression data
from microarrays(or Masspec spectrum of proteome data), Galaxy may
not be a suitable tool. For example, microarray data usually comes in
a format of M by N matrix of numerical data, with more than 10,000
rows and hundreds of columns. The display of Galaxy history frame is
not suitable for the display of such data. The statistical tools and
graph data tools in Galaxy are clearly designed for sequence data,
because in those tools, we cab only do column-wise statistics/
graphics. The query tools in Galaxy are limited to simple queries,
where combinatorial query such as “protein AND receptor” can not be
effectively performed. Again, this is not a drawback for Galaxy if
our starting point is a set of “gene identifiers” and our goal is
“sequence analysis”. Yet, I think biologist would like to start
explore the genomics data from a couple of words that describe the
“function” of a group of genes. It will also be useful to extract
data of gene expression, and to search for the correlation between
the gene expression pattern and the sequence features of those genes,
in a single platform, such as Galaxy."
15 years
positive feedback
by Ross Hardison
I unleashed a class of students on Galaxy, with options to do
anything from working through tutorials to doing something advanced.
I'm passing along some positive feedback.
"Galaxy does not seem to be difficult to use, but since I was not
sure what to try to do with a program that was new to me I decided to
go though the tutorials. The tutorials are very helpful at explaining
what Galaxy can be used to show. I think there are more features
within Galaxy than I will ever use, however, one never knows."
"I've never used Galaxy before, I thought doing the tutorial would be
most beneficial to me. I thought the tutorial was very informative
and done with a great deal of depth. I only wished that this was also
available for the UCSC web browser.
The tutorial in addition to the required reading was very helpful in
understanding the use of Galaxy. As Blankenberg et al., (in press)
explains the majority of users of the Galaxy program are biomedical
researchers, most of whom are not familiar with basic programming.
Hence in my option, such detailed tutorials are very helpful and a
great timesaver. In particular, the way in which the screenplays are
divided into specific groups a definitely less time consuming."
"In general, I found all of the tools and functions of Galaxy
simple to use and the interface easy to navigate. "
"I found this tutorial and exercise very helpful and descriptive for
using the program. I also watched screencasts 3A-3M. It was very
helpful to have all the different tools in galaxy explained in detail
and will come in handy for reference when using the program in the
future. I especially found the screencasts on uploading data and
encoding data very useful, such as the explanation of the different
analysis groups. "
Ross Hardison
T. Ming Chu Professor of Biochemistry and Molecular Biology
The Pennsylvania State University
304 Wartik Laboratory
University Park, PA 16802
e-mail: rch8(a)psu.edu
phone: 814-863-0113 FAX: 814-863-7024
15 years
genomics
by Jeff Dole
Hi,
I have a recent PhD in genetics from UC Davis. No one there, or at
the UW Madison (where I took a class in "genomics") or at Harvard
knows what it means. That has been readily admitted. Are you
talking about plumbing or electricity?
Jeff
--
15 years, 1 month
test.g2.bx.psu.edu
by Ying Zhang
Hi, if you check the history stored as "7.26" under the account
yuz111(a)psu.edu, you will find I encountered an error: "the scaffold
for hg18 chr1 does not exist".
Best,
Ying
15 years, 1 month
improvement for pasting sequences
by Radek Szklarczyk
hi,
i'd like to suggest an improvement to "Get Data/upload/paste
sequence" option. Since it's hard to enter "tab" from keyboard on web
pages (or when copy/pasting something from a web page), there should
be an option "convert spaces to tabs". That would make it possible to
enter BED format without manually replacing each space.
radek
---
Radek Szklarczyk, radek(a)cs.vu.nl, www.cs.vu.nl/~radek
15 years, 1 month
internal server error when trying to download file
by Radek Szklarczyk
I try to download alignments ( 606,582 lines, format: axt) and press
"save" link. This gives "Internal server error" after a few seconds
of waiting.
Smaller history elems (like a bed file) can be downloaded without any
problems.
You can inspect my history, user:radek, history:arf, history elems
giving errors:3-6
This used to work like a charm for even bigger files in older galaxies.
cheers,
radek
---
Radek Szklarczyk, radek(a)cs.vu.nl, www.cs.vu.nl/~radek
15 years, 1 month
