Hi,
I am relatively new to Galaxy and couldn't find an explaination on how
you envision the concepts of users/groups/roles etc...
I am managing a Galaxy instance and have different groups of biologist
(users), who should all are allowed to see the data from that group.
Then I have a group of
Thank you Peter. That's great to know.
On Feb 7, 2012, at 5:13 PM, Peter Cock wrote:
On Tue, Feb 7, 2012 at 9:52 PM, Beale, Holly (NIH/NHGRI) [F]
holly.be...@nih.gov wrote:
Hi all --
I'd like to know what programs are used when I run a tool on my data.
Ideally I'd also like to know what
hi ,
i have created a script which calls a database function(sub_id) and this
function returns multiple columns , say its return 12 columns in database , but
when i created its tool(function) in galaxy , i am able to return only 1
column(username) in galaxy tool which is not desirable result
Hello,
I am pleased to announce that registration is open for the April 2012
GMOD meeting The cost for the meeting is $40 if you register before
March 7th and $50 after. The meeting will be held April 5-6 at
Georgetown University in Washington DC, right after the Biocurator
meeting. I am also
In the new version of tophat they allow for over 3 mismatches in the initial
alignment, however your server still gives an error if you attempt to move this
over 3. This is problematic for trying to map RNAseq reads where there is
moderate divergence between the RNA and the reference genome.
Hello,
You can FTP on the command line by using:
unix% ftp main.g2.bx.psu.edu
then enter you Galaxy credentials, the exact same information used when
you log into your web account.
user = galaxy email account
pass = galaxy password
The data will be loaded onto the server under you account
Jeremy,
This is not strictly correct. Tophat/bowtie don't report mapping quality
values that are as meaningful as BWA, but there is some information in the
mapping quality values tophat reports. Tophat yields 4 distinct values for
its mapping quality values (you can do a unique count on the
Hi all,
I got the normalized values (FPKM) from cufflinks. And I want to get relative
reads counts. How can I do that?
Another question: how does cufflinks handle isoform genes while calculating the
reads counts? Or what papers can help me understand this?
Thank you very much!
Victor,
I got the normalized values (FPKM) from cufflinks. And I want to get relative
reads counts. How can I do that?
It's not clear to me what you're looking for. FPKM is a normalized read count
metric where the F stands for fragment, which is a single read (or half of a
paired read).
Dear Jeremy,
Sorry, I didn't expressed my question clearly. I got the FPKM normalized values
for each gene from cufflinks. And I want to get the original reads counts that
were not normalized from cufflinks. Could you please tell me how to get those?
Thank you very much!
Victor
Reads are probabilistically assigned, so raw read counts are not available from
Cufflinks.
Recovering raw fragment counts could be done by reverse-engineering the FPKM
value, but Cufflinks doesn't do this for you. If you choose to do this, keep in
mind that Cufflinks uses an effective
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