Help with Summary Statistics
by D. A. Cowart
Hello,
I am attempting to use Galaxy to calculate the mean sequence read
length and identify the range of read lengths for my 454 data. The
data has already been organized and sorted by species. The format of
the data is as follows:
>HD4AU5D01BHBCQCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC
>HD4AU5D01A093MCTCTGTCGCTCTGTCTCTCTTCTCTCTCTCTCTCTCT
etc...for each species
I have attempted to use the "Summary Statistics" button, however it
appears to only be for numerical data and not sequence data. Is this
tool/task available
via Galaxy?
Thank you,
Dominique Cowart
User name: dac330
7 years, 2 months
SNP finding
by Xiefan Fang
Dear galaxy users,
We have done deep sequencing on some known genomic loci using
Hiseq2000. I have already mapped the reads to the reference sequences by
using Galaxy. In the next step, I want to find SNPs and calculate the SNP
percentage within the reads. There are 500,000 to 1,000,000 reads per
biological sample. Can I do it with galaxy? If not, is there other programs
available in windows? Considering that I am not very familiar with
programming.
Thanks,
Xiefan
University of Florida
7 years, 7 months
extracting a subset of sequences from a very large fasta file(1.5 million)
by Perumal Vijayan
I have successfully uploaded a large fasta file (2.5 million genomic
sequence contigs) onto Galaxy server. I wish to extract a subset of
sequences from this file. I have a list of the fasta headers. Is there a
way I can accomplish this on Galaxy?
--
Perumal Vijayan
Saskatoon
Canada
8 years, 5 months
Re: [galaxy-user] Batch jobs...
by Neil.Burdett＠csiro.au
Do i need to modify a setting in universe_wsgi.ini or somewhere then ? As I attach screenshots of what I've got (I have a recent subversion checkout)...
Thanks
Neil
[cid:image001.jpg@01CDB754.FC6C6330]
[cid:image002.jpg@01CDB754.FC6C6330]
8 years, 6 months
History Pane empty?
by jason gagliano
Hi
I just had a quick question. My History pane to the right of my Galaxy
account on the web suddenly was empty when I logged in. I noticed that I
can still find all my datasets under "Saved History" or "Saved Datasets"
but nothing will show up now in the history pane. This is true even when I
upload a new data set.
Any thoughts on the problem and a solution?
Thanks
Jason
P.S. I have read all I could find on the topic in the help sections before
asking this question. But I could not find anything that worked for me
(like simply deleting cookies). I am relating this to say that I am trying
to be a good citizen by reading first and then asking questions :0)
8 years, 8 months
Re: [galaxy-user] Analysis in queue but not running
by Dave Clements
Hi Lew,
CC'ing the galaxy-user list because I am assuming that your question is
about the free public server ("Main") @ usegalaxy.org / main.g2.bx.psu.edu.
If you have any future questions about Main, please post them to
Galaxy-User so that others can see the question and respond.
If I am reading the qstat output correctly, there are currently ~140+ jobs
in the NGS queue, which means that Main is currently under very heavy
load. The best thing to do is let the jobs sit in the queue. Killing and
restarting them bumps them to the end of the queue.
We are currently discussing a number of options for letting users know in
situations like this, that while the job is not currently running, it is in
the queue, and is moving forward.
Thanks,
Dave C
PS: and the number of jobs in the queue has dropped by 2 since I started
typing this email.
On Fri, Nov 30, 2012 at 10:05 AM, Lewis Bowman <lbowman(a)mailbox.sc.edu>wrote:
> I have tried repeatedly to run Cuffdiff using cuffmerge output (38) and
> cufflinks output (25 and 29). In every case the job does not begin to run
> and status says"Job is waiting to run." Has Galaxy been down for the last
> several days? I am unsure what to do since I have received no error
> message. Thanks for you help.
>
> Lew Bowman
>
> --
> Lewis H. Bowman
> Department of Biological Sciences
> University of South Carolina
> Columbia, SC 29208
> PH: 803-777-5157
> FAX: 803-777-4002
> EMAIL: lbowman(a)mailbox.sc.edu
>
>
--
<http://galaxyproject.org/wiki/GCC2012>http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
http://wiki.galaxyproject.org/
8 years, 8 months
Cuffdiff tracking file does not report all genes and trancrips from reference annotation?
by Wei Liao
Hi, Galaxy user.
I ran into a problem when using Cuffdiff 1.2.1 in Galaxy local instance to
check differential expressed genes in my samples.
I have 3 normals and 6 cancers samples, I did the following:
- After tophat for each samples, run cufflink with refseq annotation which
has 25266 genes and 43091 transcripts
- cuffmerge all cufflink outputs contains 58112 lines
- run cuffdiff with 3 normals as triplicate and compare to each cancer
sample.
Suprisingly, I fould out that the tanscripts tracking file, gene tracking,
CDS tracking only has 2000 genes and 4000 transcripts. So the cufflink only
compare 2000 genes and 4000 transcripts between samples.
The question I want to ask here is that *why are the rest of the genes and
transcripts not being tested and included in the tracking files?* Do you
know what cause this kind of problem?
Thanks,
Wei
--
Wei Liao
Research Scientist,
Brentwood Biomedical Research Institute
16111 Plummer St.
Bldg 7, Rm D-122
North Hills, CA 91343
818-891-7711 ext 7645
8 years, 8 months
User's information
by Sachit Adhikari
Where are the user's information stored in Galaxy? I can't find the
information in universe_wsgi.
Regards,
Sachit
8 years, 8 months
