Hi All,
I have a very basic question about parameters for running TopHat.
I have datasets of single-end reads. These datasets were generated with
Illumina Genome Analyzer IIx. Which "Library Type" should I choose to run
Tophat?
Thanks.
Best,
Jianguang
Hi, I am relatively new to Galaxy. I would like to set it up as an apache
password protected site. I have tried to do it, but I realize now that it
has its own server built-in and that it is ineffective to set up .htaccess
because it isn't reading .htaccess (or so I think).
More information: Apa
Hello Jianguang,
This depends on how the library prep was done (which protocol was
followed). Some preserve strand and some do not. If you did not prepare
the data yourself, then the data source should be able to provide you
with this information.
Hopefully this helps,
Jen
Galaxy team
On 4
Hello Lee,
Please see the section " External user authentication" on this wiki:
http://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy
If you still need help, posting this question over on the
galaxy-...@bx.psu.edu mailing list (but not cross-posting) with more
details about what you have t
Hi Gema,
The histogram tool has the columns labeled on the tool's form - there
are a few different values that you could pull out and graph, using
others as labels, but last one is the coverage for that region of the
chrom. The second tool's output is a bedGraph file, the format is also
defin
I have looked through the metagenome tools and looked at the tutorials, and was
wondering how one could pull out reads that contain specific protein domains or
COGS. Blastx is not possible (?) but megablast could get GI codes, and these
could potentially be used to retrieve CDD information. I j
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