get wig file after tophat
by Ying Zhang
Hi:
I am using tophat in galaxy to analyze my paired-end RNA-seq data and find out
that after the tophat analysis, we can not get the wig file from it anymore
which is used to be able to. Do you have any idea of how to still be able to
get the wig file after tophat analysis? Thanks a lot!
Best
Ying Zhang, M.D., Ph.D.
Postdoctoral Associate
Department of Genetics,
Yale University School of Medicine
300 Cedar Street,S320
New Haven, CT 06519
Tel: (203)737-2616
Fax: (203)737-2286
11 years, 2 months
2011 Galaxy Community Conference, May 25-26, Lunteren, The Netherlands
by Dave Clements
Hello all,
We are pleased to announce the *2011 Galaxy Community Conference*, being
held *May 25-26 in Lunteren, The Netherlands*. The meeting will feature two
full days of presentations and discussion on extending Galaxy to use new
tools and data sources, deploying Galaxy at your organization, and best
practices for using Galaxy to further your own and your community's
research.
*Link: http://galaxy.psu.edu/gcc2011/
*
*Overview
*This event aims to engage a broader community of developers, data
producers, tool creators, and core facility and other research hub staff to
become an active part of the Galaxy community. We'll cover defining
resources in the Galaxy framework, increasing their visibility and making
them easier to use and integrate with other resources, how to extend Galaxy
to use custom data sources and custom tools, and best practices for using
Galaxy in your organization.
Additional topics include, but are not limited to:
* Talks submitted by the Galaxy community
* Integration of tools (including NGS analysis tools) and distributed job
management
* Deployment of Galaxy instances on local resources and on the Cloud
* Management of large datasets with the Galaxy Library System
* Using the Galaxy LIMS functionality at NGS sequencing facilities
* Visualizing Data without leaving Galaxy
* Performing reproducible research
* Performing and sharing complex analyses with Workflows
* An "Introduction to Galaxy" session, offered on May 24, for Galaxy
newcomers.
*Registration
*The conference fee is €100 on or before April 24, and €120 after that. The
meeting is being held at the Conference Centre De Werelt in Lunteren, The
Netherlands, which is also the conference hotel. You are encouraged to
register early, as space at the hotel (and at the "Intro to Galaxy" session)
is limited and is likely to fill up before the conference itself does.
*Link: http://galaxy.psu.edu/gcc2011/Register.html
**
Abstract Submission
*Abstracts are now being accepted for short oral presentations. Proposals
on any topic of interest to the Galaxy community are welcome and
encouraged. The abstract submission deadline is the end of February 28.
*Link: http://galaxy.psu.edu/gcc2011/Abstracts.html
*
*Sponsors
*The 2011 Galaxy Community Conference is co-sponsored by the US National
Science Foundation (NSF), and the Netherlands Bioinformatics Centre (NBIC).
NBIC is a collaborative institute of the bioinformatics groups in the
Netherlands. Together, these groups perform cutting-edge research, develop
novel tools and support platforms, create an e-science infrastructure and
educate the next generations of bioinformaticians.
*Links: http://www.nbic.nl/ and http://www.nsf.gov/
*
We are looking forward to a great conference and hope to see you in the
Netherlands!
The Galaxy and NBIC Teams
--
http://galaxy.psu.edu/gcc2011/
http://getgalaxy.org
http://usegalaxy.org/
11 years, 2 months
Re: [galaxy-user] Adding the Hydra genome to Galaxy
by Jennifer Jackson
Hello Rob,
We will add this to our to-do list for new genomes. Thanks for sending
the Genbank information!
Next time, if you could send requests to galaxy-user, that would be very
helpful for the team.
Best,
Jen
Galaxy team
On 1/3/11 12:37 PM, Rob Steele wrote:
> Hi Jennifer,
> Would it be possible to get the Hydra genome assembly added to Galaxy?
> It has been published and is available in GenBank under accession number
> ABRM00000000.
>
> Cheers,
> Rob
>
> Rob Steele, Ph.D.
> Professor
> D240 Medical Sciences I
> Department of Biological Chemistry
> School of Medicine
> University of California, Irvine
> Irvine, CA 92697-1700
>
> phone: 949-824-7341
> e-mail: resteele(a)uci.edu
> fax: 949-824-2688
> web: http://polyp.biochem.uci.edu/wiki/index.php/Main_Page
>
--
Jennifer Jackson
http://usegalaxy.org
11 years, 3 months
Cleaning of fastq files
by Felix Hammer
Hi,
is there a way to clean fastq files (filter Poly-A etc.) with Galaxy?
Haven't found anything so far. Also if you generally know good tools plz
answer.
Have seen lots of stuff for fasta and qual files but not for fastq.
Thx,
Felix
11 years, 3 months
Problems with the Groomer
by Felix Hammer
Hi,
I'm experiencing some strange problems with the fastq groomer.
Trying to groom my files I get the following error:
"Traceback (most recent call last):
File "/galaxy/home/g2main/galaxy_main/tools/fastq/fastq_groomer.py", line 37, in
if __name__ == "__main__": main()
File "/galaxy/home/g2main/galaxy_main/tools/fastq/fastq_groomer.py", line 18, in main
for read_count, fastq_read in enumerate( fastqReader( open( input_filename ), format = input_type ) ):
File "/galaxy/home/g2main/galaxy_main/lib/galaxy_utils/sequence/fastq.py", line 452, in __iter__
yield self.next()
File "/galaxy/home/g2main/galaxy_main/lib/galaxy_utils/sequence/fastq.py", line 448, in next
rval.assert_sequence_quality_lengths()
File "/galaxy/home/g2main/galaxy_main/lib/galaxy_utils/sequence/fastq.py", line 142, in assert_sequence_quality_lengths
assert qual_len == seq_len, "Invalid FASTQ file: quality score length (%i) does not match sequence length (%i)" % ( qual_len, seq_len )
AssertionError: Invalid FASTQ file: quality score length (63) does not match sequence length (36)"
I've double checked the file and it should be ok.
Any ideas?
thx,
Felix
11 years, 3 months
Import data in RGenetics
by BAULANDE Sylvain 211527 Partnerchip
dear Galaxy users,
I would like to import genotyping data in Rgenetics and I can't succeed.
I have ped file and map file, I try to import them in lped format but it didn't work ...
Anybody with experience can help me to solve this issue ?
Many thanks in advance,
Best regards,
Sylvain
11 years, 3 months
Problem Adding a Custom Build in Trackster
by Liisa Koski
Hello,
I am trying to 'Add a Custom Build' to my local instance of
Galaxy/Trackster. There seems to be a problem when I enter the chromosome
length info, both when I paste directly on the screen and when I use the
upload button (for the .len file). After I press Submit I can see the Name
and Key info that I specified but it always says that the 'Number of
Chroms' is 0.
Is there a bug or I am doing something wrong?
Thanks for you help,
Liisa
11 years, 3 months
Join and Sort in Galaxy
by Felix Hammer
Hello,
I have some questions about the Join and Sort tools in Galaxy.
How are they implemented? Just the standard unix sort and join?
I have a quite large tab file (~1,5 million lines), I want to join with a
somewhat smaller file (~20 000 lines).
How long will this approximately take? Is there a way to view the progress?
Can I gain performance if do a sort on the column I want to join?
thx,
Felix
11 years, 4 months
how to find out the gene_ID correspond to CUFF ID
by Ying Zhang
Dear Everyone:
I have got one output file after I run Cufflink which contain gene expression
information. However, I found out for each gene_ID, it has the format like,
CUFF.1151175, do you have idea of how to find out the offical gene ID
correspond to this CUFF ID? Thank you very much!
Best
Ying Zhang, M.D., Ph.D.
Postdoctoral Associate
Department of Genetics,
Yale University School of Medicine
300 Cedar Street,S320
New Haven, CT 06519
Tel: (203)737-2616
Fax: (203)737-2286
11 years, 4 months
