Dear Noa,
I also feel the same. So I think it would be better to use these three steps
remove sequencing artifacts
then trim the sequences by from the 5' end or if needed from the 3'end also
(2-5 bases, depending on your sequence quality)
finally filter the sequences by quality (I used the
Dear Noa,
Bowtie in
--besthttp://bowtie-bio.sourceforge.net/manual.shtml#bowtie-options-bestmode
eliminates strand bias by forcing Bowtie to select one strand or the
other with a probability that is proportional to the number of best sites
on the strand.
try with this mode. I am also trying to
Hello
I am a relatively new user on Galaxy and I had a question regarding Fetching
Taxonomic Information. It is great that I can retrieve all of the hits for
each sequence, but I cannot seem to find an option to also provide how accurate
of a match it is to the given taxon. For instance, a
I am running a local copy of Galaxy, last ran 'hg pull -u' on 2/20/12.
I am trying to enable use of Mpileup for SAM Tools, and have added the entry
for the samtools_mpileup.xml file in tool_conf.xml. However, when I startup
Galaxy, the link for Mpileup does not appear in the Tools pane, and I
Hello Mike,
I am going to move your question over to the galaxy-...@bx.psu.edu
mailing list, which is for the discussion of local instance questions.
Some things to double check:
SAMTools is already set up correctly, with indexes?
http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup
- see SAM
Vincent
Great question!!! And a follow up for me, is how to purge the conserved
sequences. Presently the current data set I have from Fetch is likely
to be 99% composed of incorrect taxon just because of conserved
sequence. So, how do you select just unique sequences (ie those that do
not
Hello all,
Did this issue get resolved?
If Sandrine was right about there being an off by one error in GI number in
the BLAST tabular output, it could be a bug in 'legacy' blastall command.
I say 'legacy' BLAST because that's what Galay's NGS 'megablast' tool
is using internally (as opposed to
Hi Raj,
Thanks for reporting, this issue has been resolved in changeset
6778:35be930b21be. Please let us know if you encounter further issues.
Thanks for using Galaxy,
Dan
On Mar 1, 2012, at 3:30 AM, Praveen Raj Somarajan wrote:
Hello,
I'm facing an issue with Depth Of Coverage tool
Hi,
I hoped that someone could shed some light onto this .
I am attempting to map a set of 2x 150 illumina PE data from a DNA resequencing
project.
The run had an issue where the quality of the last 50 or so reads of the second
run tail off quite considerably.
I thought to trim the second
Thanks Jennifer, I already uncomment and add my email address but still the
admin link does not appear. I then registered my email in users and logged in
with that email address and I still don't see the link.
when I type /admin at the of the url it says that I have to be logged in as an
Do you restart your Galaxy server when you make changes to universe_wsgi.ini
(like adding / uncommenting email addresses for the admin_users setting)?
On Mar 1, 2012, at 12:56 PM, Alejandra Rougon wrote:
Thanks Jennifer, I already uncomment and add my email address but still the
admin link
I did close the web browser and opened it again
was that enough?
From: Greg Von Kuster g...@bx.psu.edu
To: Alejandra Rougon alerou...@yahoo.com
Cc: Jennifer Jackson j...@bx.psu.edu; galaxy-user@lists.bx.psu.edu
galaxy-user@lists.bx.psu.edu;
No, you'll need to stop and restart your Galaxy server.
On Mar 1, 2012, at 2:01 PM, Alejandra Rougon wrote:
I did close the web browser and opened it again
was that enough?
From: Greg Von Kuster g...@bx.psu.edu
To: Alejandra Rougon alerou...@yahoo.com
Cc: Jennifer Jackson
Hello Dan,
But, I am currently using the latest update of Galaxy (as 'hg incoming' says
'no changes'). Just to clarify one thing: which repository should I clone -
https://bitbucket.org/galaxy/galaxy-dist/ (mentioned in GetGalaxy.org) OR
http://www.bx.psu.edu/hg/galaxy/ (mentioned in
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