I have been using cufflinks on Galaxy Main. I have downloaded the files generated but they do not correspond to the file names expected by cummeRbund.
cummeRbund expects 4 tracking files (e.g isoforms.fpkm_tracking) , 4 .diff files (e.g isoform_exp.diff).
Here is a trimmed version of the output I download, grouped by what Im guessing is the tracking, diff and usage files:
Given that cummeRbund is a common next step in the workflow, is there an option to save the output in the expected format, perhaps with a galaxy history number prepend? I'm not sure which files are to be renamed and to what name and it seems that one file is missing.
If there were a cummeRbund implementation on Main it probably wouldn't matter as much but until that happens, I (and i'm guessing other newcomers) would appreciate the help!
I'm trying to joint two large intervals (one with 800,000 intervals and the other with about 350,000 intervals) using operates on intervals > join tool . I have no idea how long it should takes normaly. Two days have past and it is still runnig. Is there any limitation in file size for this tool?
Any help would be appreciated.
PhD student of Medical Genetics
Department of Medical Genetics
Shahid Beheshti's university of Medical Science
I have a student that found an unexplained discrepancy between the results produced by the "Operate on Genomic Intervals" (OGI) intersect operation versus the OGI join operation. In particular, we know for certain that there are exactly 1105 intersection of at least 1bp between the two files we are testing, as we have confirmed this with our own bedtools and the ucsc table browser. An example intersection (intersecting positions: 10012008 - 10012013):
chr1 10012008 10012021 5.6186
chr1 10011813 10012013 5_Strong_Enhancer 0 + 10011813 10012013 250,202,0
However, OGI intersect find 0 intersections between the files (settings: return overlapping intervals, >= 1bp). In an effort to make sure we didn't goof up on file formats (BED) or genome builds (hg19), we tested the exact same two files with the OGI join operation and found 1105 intersections as expected.
I also tested the files with the bx-python bed_intersect.py and bed_intersect_basewise.py scripts and get the expected results.
Does anyone have a suggestion for how to resolve this?
Thanks for your help and for providing such a fantastic resource to the genomics community.
Let's say that I have results produced from a step in multiple different histories and that I now want to gather these results into a new history so that they can be joined. Is there a way to do this without exporting results to my desktop and then uploading?
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If you have other sequence types, there are other alignment tool choices
on the public Main server. The est2genome tool has a fairly specific
use, so I thought that this was your input/goal.
For ChIP-seq, RNA-seq, or other NGS datatypes, please see the tools
under 'NGS: Mapping' and 'NGS: RNA Analysis'. We have tutorials for
these tools - from the top menu bar follow 'Shared Data -> Published
Pages". Good places to start are 'Galaxy Exercises', 'Galaxy RNA-seq
Analysis Exercise', and 'Using Galaxy' (but review the others as wanted,
I am not sure what type of data you are working with). More tutorials
are in our wiki here:
Other public Galaxy sites offer specialized tools for working with
certain data types - the best way to find out what they have to is visit
them and review. We keep a list of links in our wiki here:
Good luck with your project! Next time, or if you have followup, please
be sure to leave the mailing list in the cc to help us with tracking.
On 2/4/13 8:08 AM, John Phillips wrote:
> Are you sure that there is no way for me to align multiple sequences? I
> apologize if I did not use the correct technical language, but from what
> I understand, everyone seems to be citing you guys for sequence alignments.
> Thank you,
> On Sun, Feb 3, 2013 at 1:34 PM, Jennifer Jackson <jen(a)bx.psu.edu
> <mailto:firstname.lastname@example.org>> wrote:
> Hi John,
> The current link is:
> We changed our wiki base and many of the older links do not
> redirect. I'll let our wiki admin Dave know about this and see what
> can be done. If this comes up again soon, the base always redirects
> to "http://galaxyproject.org -> http://wiki.galaxyproject.org"__,
> and clicking into "Learn" will likely take to you want to go - the
> primary hub page for user documentation - including the links in
> tutorials (plus the wiki side navigation bar with a few different
> search options).
> And is true that we do not offer large scale EST to genomic
> alignment on the public server. Galaxy choices such as
> BLAST+/Megablast are for use with a local or cloud Galaxy instance.
> When using a local instance, the tool wrapper can be obtained from
> the Tool Shed (http://toolshed.g2.bx.psu.edu__). A cloud ami would
> have these tools as part of the package. You can also check the Tool
> Shed for other options - more are added all the time.
> Local: http://getgalaxy.org
> Cloud: http://usegalaxy.org/cloud
> Hopefully this helps,
> Galaxy team
> On 2/2/13 3:17 PM, John Phillips wrote:
> To Whom it May Concern:
> I am using the Galaxy interface, and according to the tutorial
> screencast, I should be able to upload my own reference genome. The
> address given in the tutorial
> <http://galaxyproject.org/FTPUpload>) leads
> to a 404 file not found page. I was wondering if there is an
> site that can allow me to do this.
> Also, I tried to use the est2genome tool in order to try and
> align my
> uploaded sequences. It would only allow me to compare two
> sequences at a
> time. Is it possible to align a larger number of sequences at
> once? I
> understand there are other programs that allow for this kind of
> procedure (e.g. Sequencher), but I would like to do this in Galaxy.
> Thank you for your time,
> -John G. Phillips
> Graduate Research Assistant
> University of Tulsa
> 231-233-6914 <tel:231-233-6914>
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org <http://usegalaxy.org>. Please keep all
> replies on the list by
> using "reply all" in your mail client. For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
> Jennifer Hillman-Jackson
> Galaxy Support and Training
> -John G. Phillips
> Graduate Research Assistant
> University of Tulsa
Galaxy Support and Training
To Whom it May Concern:
I am using the Galaxy interface, and according to the tutorial screencast,
I should be able to upload my own reference genome. The address given in
the tutorial (http://galaxyproject.org/FTPUpload) leads to a 404 file not
found page. I was wondering if there is an alternative site that can allow
me to do this.
Also, I tried to use the est2genome tool in order to try and align my
uploaded sequences. It would only allow me to compare two sequences at a
time. Is it possible to align a larger number of sequences at once? I
understand there are other programs that allow for this kind of procedure
(e.g. Sequencher), but I would like to do this in Galaxy.
Thank you for your time,
-John G. Phillips
Graduate Research Assistant
University of Tulsa
The tutorial you were looking at was made using one of our local Galaxy
instances, in advance of updating the main public server. The main server
already includes most of the tools used in the examples, but two of the
format conversion tools ("MasterVar to gd_snp" and "pgSnp to gd_snp") are
not posted there yet.
I apologize for the delay. We are in the process of moving some of the tools
from the Phenotype Association section of the toolbox to the Convert Formats
section, while simultaneously migrating those and the rest of the Phenotype
Association tools from their current, manually configured installation method
to the new Galaxy Tool Shed paradigm. We have encountered some technical
difficulties with that, but we hope to have the update accomplished within
the next few weeks.
If you need it sooner, let me know and I'll send you the underlying Perl
script for the "pgSnp to gd_snp" tool, so you can run that locally to
convert your file and then upload the output to your Galaxy history.
Thanks for your patience!
> ---------- Forwarded message ----------
> From: Sheehan, Michael - (michaelsheehan) <michaelsheehan(a)email.arizona.edu>
> Date: Wed, Jan 30, 2013 at 1:30 AM
> Subject: [galaxy-user] Converting files to gd_snp format
> To: "galaxy-user(a)lists.bx.psu.edu" <galaxy-user(a)lists.bx.psu.edu>
> I would like to convert VCF files to gd_snp format to be used in some
> population genomic analyses. A tutorial online makes it seem like this
> is the correct path to follow to conduct such analyses:
> I have been using Galaxy on the free public server and this tools does
> not appear to be present anywhere. Does anyone know where the tool has
> gone or is there a way to add the needed tools back?
We have galaxy-dist-17d57db9a7c0 installed on our Mandriva 2009 64bit.
There are 2 big fasta files,
file A is 4.4G and file B is 3.3G
which I tried to download without success.
I've used browser download,including mozilla,IE and Chrome,also from
suggestion by Jennifer: linux command: wget and curl -O.None of them work.
For file A,the downloaded file size is always 450M(9% of total size),no
matter which way ( mentionedabove )I use,
For file B,the downloaded file size is 0 byte.
Following is the error report by :curl -O
curl: (18) transfer closed with 4294967296 bytes remaining to read
Any help will be very appreciated.