Visualization > New Track Browser dropdown menu too long
by Kevin Lam
I found the dropdown menu list to be too long to be effectively used
especially when viewed i chrome (browser) I can only see 5 genomes at a time
and the ordering of the genomes isn't intuitive.
Can I suggest that a frequently used genomes list be in the rest of the page
so that it is easier to use for most users? like a table of common genomes
to immediately create a new track browser from there?
Cheers
Kevin
10 years, 11 months
user specific access/options
by Petr Novak
Hi everybody,
I am developing the application on Galaxy server. One of the requirement is
to create user specific list of options. Is it possible to access somehow
$__user_email__ in <options> tag or in <conditional> ?. I did not found
documentation how to used cheetah in galaxy tool xml files but from files
provided with galaxy, cheetah is used only in <command> and <config> tag. Is
that rigth? If it can be used in any part of xml definition file it would
make much easier to generate xml dynamicaly based on the $__user_email__
Does anybody have an idea how to manage this problem?
Petr Novak
10 years, 11 months
Thanks from Di Nguyen. U of Washington
by Jennifer Jackson
Hello Di,
Both Bowtie and Tophat will map sequences, with Tophat being preferred
for RNA-seq data. If you wish to do downstream analysis, then using the
Cuff* tools would be the next steps. Each of these tools has an
associated help description that explains the inputs/outputs.
Thanks for using Galaxy,
Jen
Galaxy team
ps. Please send all questions directly to the mailing lists unless they
contain private data/links.
On 9/1/11 10:45 AM, Di Nguyen wrote:
> Hi Jen,
>
> Thank you very much. I already used Galaxy to prepare the mapping by
> bowtie for solid. I saw the tophat for solid on the test server and will
> try it. Do I need to run cufflink after that?
>
> Please accept my utmost appreciation!
>
> Di
--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/Support
10 years, 11 months
Customize Annotated refgenome in Galaxy
by Anton Nekrutenko
Qiang:
I'm reposting this question to the galaxy-user mailing list.
Thanks!
anton
> Dear Anton,
>
> I am a PhD student in the Matrin-Luther University Halle-Wittenberg focused on honey bee Ecology.
>
> Galaxy is a very flexible tool to do RNA Seq analysis. I have a problem and need your help. The galaxy provide build in annotated reference genome of honey bee (2005). This is a old version and the lastest version (2011) has much higher resolution (http://www.ncbi.nlm.nih.gov/nuccore?term=CM000054:CM000069[PACC]). I tried to bulid a customized annotated reference genome. First, I upload the annotated reference genome (.gb file), but can not choose it when I map the read (Tophat for Illumina). Then I upload the reference genome without annotation (.fasta file), it works. But I need the annotation of the genes to analyze the differencial expression.
>
> We are very interested in galaxy and use it in our research analysis. Hope you can help us solve this problem.
>
> Expecting your reply!
>
> All the best,
> Qiang
>
> ****************************************
> Qiang Huang
> Institut für Biology/Zoologie, Molekulare Ökologie, Martin-Luther-Universität Halle -Wittenberg
> 06099, Halle, Germany.
> Honeybee Research Institute, Jiangxi Agricultural University, 330045, Nanchang, China.
> http://www.mol-ecol.uni-halle.de/staff/huang-q/
>
10 years, 11 months
RNAseq for Solid data
by Di Kim Nguyen
Hi,
I needed help in crunching RNA-seqs done with solid platform. I have fasq
files. Please give me the steps necessary in this process to get the fpkm
from cufflink? This is mouse data.
Thank you very much, please accept my appreciation.
Di Nguyen
U of Washington
10 years, 11 months
