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?
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?
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,
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!
I'm reposting this question to the galaxy-user mailing list.
> 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 Huang
> Institut für Biology/Zoologie, Molekulare Ökologie, Martin-Luther-Universität Halle -Wittenberg
> 06099, Halle, Germany.
> Honeybee Research Institute, Jiangxi Agricultural University, 330045, Nanchang, China.
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.
U of Washington