Hello Giuseppe,
Please try two things:
1. At the top of the history panel is a small double arrow refresh
icon. Click this to see if it updates the view. If not, click on the
very top Galaxy masthead icon. This should not be necessary any
longer, but try it anyway.
2. Double check that the
set delivery on
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Hi Maria,
This message indicates that an error occurred on the cluster node
processing the job. Normally these are not linked to inputs or tools and
the general solution is to re-run the job. Please give this a try today
- it is possible the error was linked to recent transient server issues.
Hello,
I am fairly new to galaxy and I am trying to use bowtie2 to map my reads
against a custom genome (specifically a ribosomal RNA fasta file). I have
formatted the file as suggested in the Galaxywiki ect and I am still
getting the following message: Job output not returned by PBS: the output
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Hi,
I have worked so far on the free web-based version of Galaxy; now I have
installed Bio-Linux 7, and there is Galaxy in there as well. However, I cannot
access to my data (stored on the web version of Galaxy) using Galaxy on Bio
Linux. If it is possible, does anyone know how to do it?
Cuffmerge does some additional steps that Cuffcompare does not; specifically,
Cuffmerge attempts to remove assembly artifacts:
http://cufflinks.cbcb.umd.edu/manual.html#cuffmerge It's likely that the
(presumed) artifacts removed by Cuffmerge account for the differences that
you're seeing.
Security warning: DO NOT CLICK on the link in this thread.
Eric Guo - it is likely that your original sending hotmail email account
has been compromised. We have removed it from the galaxy-u...@bx.psu.edu
mailing list to prevent further unmoderated posts until the problem is
cleared.
Hi,
I am performing online tophat on 5 different samples which I want to compare
for gene expression. Is there any simple way, after the end of tophat for all
of them, with which I can have an excel table with the 5 samples and their hits?
Something similar to this
Vevis1
Vevis2
Vevis3
Kristis,
This data is available further downstream in an RNA-seq analysis pipeline,
specifically, as output from the Cuffdiff tool. Take a look at the page for
more details:
https://main.g2.bx.psu.edu/rna-seq
Best,
J.
On Nov 9, 2012, at 3:42 AM, Vevis, Christis wrote:
Hi,
I am
I am new to the NGS analysis. I need help to solve this problem.
As shown in my previous emial/question shown below, I have some paired-end
datasets at FASTQ format, and I have problem to split each of these datasets
into two datasets (one forward and one reverse).
Jennifer instructed me
Hi Megan,
I ran a few tests and found that changing the file suffix to .txt when
using the autodetect upload type function speed up the loading process
considerably. As the final result is an identical Galaxy dataset to what
is produced with using the existing suffix, this is something I
I have been unable to upload data files into Galaxy Main since Friday 18th May
2012. Today is my fourth day of attempting uploads. Refreshing and leaving the
files to upload overnight does not work.
Although Jennifer has stated the bug has been fixed at 5.30pm today I am still
unable to upload
Hello Megan,
Are you still experiencing problems now? Galaxy may have been busy
immediately following the resolution of the cluster problem, although
your problem does appear to be unrelated.
It sounds like you are uploading file through a browser. A better choice
would be to use FTP. This
Hi,
I have hit a brick wall when trying to convert wig files from the GEO
to bigwig files. Each time I try (and I have tried many times since
October), I get the same error. For example, here is a downloaded wig
file, that I assigned to the mouse mm8 genome, and the error I got
when I
Hi,
I read on Readme for MACS that: For the experiment with several
replicates, it is recommended to concatenate several ChIP-seq treatment
files into a single file.
Now, I have illumina ChipSeq data: two files for IP samples and two files
for Control samples. Is It right to use Concatenate
Dear All
How can I de-subscribe from the mailing list?
Any help would be appreciated
Kind Regards
M. J
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--
Y.P.V.S.Raja Raghava Rao
Research Scholar
Dr.K.Sreenivasulu Lab
Dept.of Animal Sciences
School of Life Sciences
University of Hyderabad
ypvs...@gmail.com
9989733698
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Hi Jeremy,
I tried to run cufflinks to assemble transcripts after running Tophat against
my own reference. This error was encountered.
What was wrong? How to fix it?
Error running cufflinks. [21:01:14] Inspecting reads and determining fragment
length distribution.
Processed 11130 loci.
Hello Tarek,
If you want to reduce the number of identical reads, then please see the
tool FASTA manipulation - Collapse sequences. Converting formats
would be necessary, the tool Tabular-to-FASTA can perform this operation.
Best,
Jen
Galaxy team
On 8/2/11 3:57 PM, tarek addwebi wrote:
Aaron Jex
Verzonden: dinsdag 24 mei 2011 1:40
Aan: galaxy-u...@bx.psu.edu
Onderwerp: [galaxy-user] (no subject)
Hi,
Can't seem to find an answer to this on your wiki site and it's not in the
tutorial. I would like to filter my 454 reads for high quality regions, rename
the resulting sequence
On Tue, May 24, 2011 at 12:40 AM, Aaron Jex a...@unimelb.edu.au wrote:
Hi,
Can’t seem to find an answer to this on your wiki site and it’s not in the
tutorial. I would like to filter my 454 reads for high quality regions,
rename the resulting sequence fragments AND relink the new reads
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