Hi Neil,
with your current apache configuration, you should probably see Galaxy
at http://yourip/galaxy
This is due to your Rewriterule /galaxy and for that you have also set
proxy_prefix = /galaxy in your universe_wsgi.ini
You should probably remove the empty galaxy directory under /var/www
Dear All,
I am analysing RNA-seq datasets for the differential splicing events between
cell types. My reads are 36bp long. In order to increase the quality of reads,
I need to trim some nucleotides from ends. How many nucleotides can I trim? I
am afraid that if I trim too much, the reliability
Dear All,
I am analysing RNA-seq datasets for differential splicing events between cell
types.
Some of my reads contain bed nucleotides, should I run Filter FASTQ to remove
these not so good reads? If I do need to, what is the Minimum Quality
should I set for the Filter?
Thanks.
Jianguang
Dear All,
I am analysing RNA-seq datasets for differential splicing events between cell
types. These are mouse cells. Jen suggested me to use the iGenomes version of
reference GTF to take full advantage of the options in CuffDiff. My question
is: should I use this iGenome version reference GTF
Hello Jianguang,
This general protocol is also in the RNA-seq tutorial:
http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise
-- Understanding and QCing the reads
That said, I had a sample of your data from before and I ran FastQC on
it and see what you mean, the quality drops
No, no it's just internal billing within our organization. We're
charging for compute time on the cluster, not for any particular
software. No one is making any money off of Galaxy, it's just a way
to fairly divide up the compute time available to the organization.
-Greg
On Thu, Aug 23, 2012
Hi Jen,
Thanks for your help.
Do you mean that if I want to find novel isoform/splicing, I need to select
No under Use Reference Annotation when I run Cufflink, and then use iGenome
version of reference GTF when I run Cuffmerge?
Based on your information and some protocols found online, my
I completely understand what you're saying Greg and I have no doubt that your
billing only covers the maintainence costs of your cluster - and I don't want
to derail your thread because you ask a very legitimate question (to which im
afraid I dont know the answer to, and would also be
On 23 August 2012 14:39, John Jones mr.johnjo...@gmail.com wrote:
[...] knew what protection there is for the developers of software if
anyone can charge, say, $1000 for an alignment using free tools that takes
only an hour to run.
Many open source licenses will permit anyone to charge for
Anyway, back to my question. Does anyone know? Would I be better off
asking on the developer mailing list or perhaps Stack Overflow?
Thanks again,
Greg
On Thu, Aug 23, 2012 at 2:59 PM, Joachim Baran joachim.ba...@gmail.com wrote:
On 23 August 2012 14:39, John Jones mr.johnjo...@gmail.com
Hello Jianguang,
On 8/23/12 11:28 AM, Du, Jianguang wrote:
Hi Jen,
Thanks for your help.
Do you mean that if I want to find novel isoform/splicing, I need to select No under
Use Reference Annotation when I run Cufflink, and then use iGenome version of reference
GTF when I run Cuffmerge?
On Thu, Aug 23, 2012 at 8:44 PM, mailing list margeem...@gmail.com wrote:
Anyway, back to my question. Does anyone know? Would I be better off
asking on the developer mailing list or perhaps Stack Overflow?
Software licensing is a much broader issue that Galaxy, so yes,
perhaps Stack Overflow
Hi Jen,
I had a problem when I tried to run Tophat with the iGenome reference GTF.
What I did is:
1) uploaded iGenome version of mm9 genes.gtf by: Shared Data - Data Libraries
- iGenomes - click genes.gtf under mm9 - click Go for Import to
current history. The genes.gtf appeared in history and
Hi Jelle,
I'm still having issues with Apache. I've moved
RewriteEngine on
RewriteRule ^/galaxy$ /galaxy/ [R]
RewriteRule ^/galaxy/static/style/(.*)
/home/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L]
RewriteRule ^/galaxy/static/scripts/(.*)
Hello Jianguang,
Two different data are being mixed up: genome vs annotation
reference genome (format: fasta) vs reference annotation (format: GTF)
To annotation your sequences against the mm9 reference genome, choose
locally cashed and select mm9 from the pull down menu.
Then, optionally,
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