Hello Liesbeth,
Hopefully you are no longer having this problem, but we wanted to
follow-up. From our view of your account, all histories are accessible
on the Main public Galaxy server at http://usegalaxy.org.
Our sincere apologies for transient usage issues that occurred around
the time
Hello,
Please check all histories and shared histories. All data must be
permanently deleted, and no histories shared with you, to reach 0% usage.
Find all in the in the history menu under:
* Saved histories - Advanced search - status = all or deleted'
* Histories shared with me
Help is
Hello Nancy,
The attribute sounds as if it is the correct place in the reference
annotation file (the 9th field), but perhaps there are other
format/content problems with the file. Do you have a tss_id? Do you have
exons labeled?
This is the area of the manual that covers the formatting and
Hi Jennifer,
I did see tss_id in my results and also exon labels. The tss_id was
assigned during the calculation, having the numbers tss1, tss2, etc. By
saying writing codes I mean such as in the link you sent to me, there is:
*Note: *If an arbitrary GTF/GFF3 file is used as input (instead of
Hi Nancy,
It is not quite clear in which steps you used the reference annotation
or how these attributes were lost exactly. Cuffcompare is a tool in
Galaxy - but before we go any further I think that examining the history
would be the speedest path to a solution. Would you share a history
Hello L.Y.,
I just tested .bam upload using FTP (with the client FileZilla) and all
went fine. Just to confirm, you are using the public Main Galaxy server
at http://usegalaxy.org? Many of our services were down for several
hours yesterday for maintenance related reasons - if you upload
Hi Robert,
This function is not wrapped into a tool yet by the dev team. I checked
the Tool Shed as well and didn't see it there. But there is another
option to get to the same result.
The tool Text Manipulation - Select random lines from a file can be
used with a SAM file. Don't not use
Hello Vioricia,
For this question, it would be best to contact the team that is hosting
the public Galaxy site, as these are tools custom to their server. The
contact information is on the bottom of the home page:
http://unifrac.colorado.edu/
Best!
Jen
Galaxy team
On 9/25/13 1:13 PM,
Hello,
There are some tools in the group 'Text Manipulation' that do this sort
of manipulation directly. Combined, many basic unix functions can be
performed. Combine them to create custom tools using Workflows - even
place them in your tool menu for seamless access.
To move from file A to
Hello Larry,
The Manipulate Fastq tool only brings up the regular trimmer tools
again once sequence and trim are selected, so this will not work. And
a regular expression could be used as a filter, but that will not
actually trim the data.
If you choose to filter, this regular expression
You could use the adaptor clip with e.g. a custom poly-A 'adaptor'
its in FASTX-Toolkit for FASTQ data
best,
ido
On Jul 28, 2013, at 8:44 PM, Larry Simpson larrys3...@gmail.com wrote:
Hi
Is it possible to trim a variable number of a specific nucleotide from the 3'
ends of fastq RNA
Hi Kathryn,
These first three are three different types of sequence databases
available from GenBank The last is a genome assembly for the phiX174 genome.
Information about all can be found here:
http://www.ncbi.nlm.nih.gov/genbank/
There are many uses, one example is covered in our
Hello Kathryn,
Trackster is the primary data visualization tool and can be accessed
by clicking on the mini graph icon within a dataset:
or by going to "Visualization" in the upper menu bar and starting a
new track browser.
Hi Sandra,
Galaxy can certainly be used to correlate a set of unknown genomic
coordinates with another annotated set of genomic corrdinates, such as
those available from UCSC, Biomart, etc.
The tool set to look at is Operate on genomic intervals and an example
of how these tools are used,
Hi Mathew,
Regarding 1 you might want to read this thread:
http://user.list.galaxyproject.org/Problem-with-Depth-of-Coverage-on-BAM-files-GATK-tools-td4654147.html
All tools from GATK are limited to hg_g1k_v37 as far as I know.
Best,
Carlos
On Mon, Aug 6, 2012 at 10:30 AM, Mathew Bunj
Hello Mathew,
Carlos is correct the the tools in the group NGS: GATK Tools (beta)
will require that the data is mapped/associated with the reference
genome hg_g1k_v37. Belinda has offered to help with the details that
go beyond Galaxy and that is great - the GATK forum is definitely the
best
Hi Kanwar,
I found that you also posted this question and another like to the
Google group for SICER on 7/10 and received some help there:
http://groups.google.com/group/sicer-users
Glad that you were able to get the questions resolved. For others
reading this post or interested in SICER
Hello Vasu,
These databases contain sequences from all species in the divisions. The
number indicates the release version. The actual source is:
ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/
A description of each division's contents can be found at:
http://www.ncbi.nlm.nih.gov/genbank
The
Hello Shamsher,
Another user posted that they have started a Galaxy wrapper for the
Circos tool itself, but I wanted to let you know about the tool EMBOSS
- cirdna: Draws circular maps of DNA constructs.
The link on the tool's form points to all of the EMBOSS tools, including
this specific
If I may add, I believe galaxy will uncompress your files if zipped.
Unzipping a 13 GB file, will take a while.
Kev
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at
Hello Maha,
This does sound very strange. Would you please share a link to your
history so that we can examine the data and determine where the problem
originates? Please note which dataset contains this particular problem
if there are several runs from this same tool.
Use Options - Share
Hi Shamsher.
We have a small initial wrapper for circos. Its not complete yet and we
are not sure if its even possible to wrap such a complex tool in a good
galaxy UI. But if you are interested i can share our code.
Cheers,
Bjoern
I wonder if is it possible to visualize mutation data in
Hello William,
To use a custom reference genome, all you need to upload is the single
fasta file for the genome. Galaxy will do the rest and create indexes as
appropriate.
Hopefully this helps!
Thanks,
Jen
Galaxy team
On 2/6/12 11:51 AM, William Light wrote:
I recently tried to upload a
Hello Michael,
Data will count towards the disk quota when not permanently deleted.
Also, once permanently deleted, it will take a bit of time (less than an
hour to several hours) for the disk counts in the UI to update. Perhaps
this has already been resolved, but if not, hopefully the rest
Hi Rahul,
This is the maximum number of bases which can have their score not included
when calculating the result of the selected aggregation function.
For example, if you had a 5 base window with scores of 5,5,2,5 and 5, set
aggregation to min score with a specified value of 4, with the
On Thu, Nov 10, 2011 at 6:10 PM, Rena Zheng rzh...@mail.med.upenn.edu wrote:
Hi,
I uploaded a bed file to Galaxy and did some text manipulations. I want
to download the new file as a bed format that I can then open up in excel
or a text editor. However, when I save the data, it is a .tabular
Hello Xaingmimg,
When you uncompress the archive locally, does it contain a single file
with more than 5000 reads? The consistent results and even number of
reads (5000) may mean that the archive contains more than one file.
Currently, Galaxy will only load the first file in an archive.
You can download DRA files directly by FTP to Galaxy . .
Just paste the FTP address directly in the file box when using upload from
my computer
Best
Simon
On 7 November 2011 04:54, Xiangming Ding din...@ucla.edu wrote:
Hi galaxy
I am a new user of galaxy. i met a problem and didnot find
Hello Xiangmimg,
Data files can be loaded using a URL on the Get Data = Upload form.
FTP and HTTP connections are supported. This is briefly described on
that form.
If you are still having issues, there may be a problem with file
compression or the connection. Downloading locally then using
Hi
the file name is spr097786.fastq.bz2.After upload it showed
spr097786.fastq. It showed it only contain around 5000 sequence reads.
I also tried to upload through FTP. so i download the file to my
computer and then upload to FTP in galaxy. the totlal 800M file was
uploaded to the FTP
Hello,
For tools that allow a custom genome, the form will include an option to
use a Dataset from the history (or similar). Then a sub-menu will pop
up where the reference genome can be selected.
Other basics:
For the query sequences, Fastq or fasta format may be required. After
upload,
Hello Diana,
For the main public Galaxy server, an input sequence file of this size
should not be a problem when analyzed through the standard tools. Hard
quotas are not set at this time, but will be announced soon. Current
guidelines can be found at:
http://galaxyproject.org/wiki/Main
On 09/23/2011 09:26 PM, dtr...@ira.cinvestav.mx wrote:
Hi, mi name is Diana Trejo and I am working with galaxy for first time. I
would like to analyze millions of sequences in galaxy but I don´t know if
it is possible because my file is 330 MB. Are there any MB restriction for
using galaxy?
Hello Luciano,
This was a bug, fixed in galaxy-central yesterday: changeset
4212f675f95b . You can either pull the changeset into your local
instance or wait for it to be incorporated into the next distribution
(within the next few weeks).
Next time, it would be great if you would send
Hello William,
The tools in NGS: QC and manipulation, especially those in the
sub-section AB-SOLiD data can do the manipulations needed before
mapping. It may be helpful to view the screencast at
http://usegalaxy.org, center pane, quickie #9.
Hopefully this helps to get you started,
Best,
Hi Jackie,
The screencasts under Metagenomic Analyses with Galaxy specifically
use 454 data and would likely be helpful, maybe even if you have already
resolved your prior issue.
http://main.g2.bx.psu.edu/screencast
Apologies for the delay in reply, we were a bit backed up with questions
in
Hi galaxy-users
When trying to display a set of chip microarray data in UCSC main, ,
we encounter this error:
Error(s):
Error line 38879 of
http://main.g2.bx.psu.edu/root/display_as?id=3221463display_app=ucscauthz_method=display_at:
chromEnd larger than chrom chr21_random size (1679928 1679693)
Hello,
The error is indicating that the end of your dataset is larger than the
chromosome it is aligned to for this line (at least). This is expected
when attempting display of certain data types at UCSC.
This is a known issue. You can either remove these lines from your
dataset with tools
Hello Wen,
It's not necessary to send multiple emails to the mailing list; we track
incoming emails to ensure that we respond to all of them.
Your FPKM values do look high, but keep in mind that coverage is only part of
the FPKM calculation; it's also dependent on transcript length and the
Felix,
You seem to be providing the correct inputs to Cuffdiff and it appears to be
producing valid output. More information about setting parameter values and
interpreting Cuffdiff can be found in manual:
http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff
Good luck,
J.
On Jun 16, 2011, at
What version of Cufflinks is your Galaxy installation running? A recent version
(1.00 and 1.01) had a problem that was causing the splicing and promoter use
tests to have very few differentially regulated genes, according to
http://cufflinks.cbcb.umd.edu/.
-rory
On Jun 16, 2011, at 8:13 AM,
Jagat,
First, a couple housekeeping issues:
(a) the questions you're asking are better suited to the galaxy-user list
(questions about using Galaxy and performing analyses) rather than galaxy-dev
(questions about installing Galaxy locally and tool development), so I've moved
this thread to
Hey Jennifer,
I was using email/password, just tried again and I got in. Weird. Thanks
for the quick response!
Danny
On Mon, Feb 7, 2011 at 3:21 PM, Jennifer Jackson j...@bx.psu.edu wrote:
Hello Danny,
Are you connecting to main.g2.bx.psu.edu and using your Galaxy credentials
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