Thanks  Mete and Jenifer for your information.
Last time, I did mRNA sequencing analysis and decided to go with
TopHat>Htseq>DESeq for DE genes. Just because the results match up quite
nicely with my qPCR validation. Although Cuufflink/Cuffdiff produced
results with quite similar trend with DESeq, It seem to me that Cuffdiff
tend to inflate the fold-change and is not good at statistical analysis.
Thanks Jenny and Ross.
Anyway, about the miRNA I am working on now. My miRNA data is 51bp,
single-ended.  I am going to cut adapter using FASTX-toolkit and align
reads using Novoalign ( as Mete suggests)  and  Bowtie.
Just have a question for now: my 3' adapter sequence is :
5-rAppAGATCGGAAGAGCACACGTCT-NH2-3.
How many bases  should I put in the " Enter custom clipping sequence" ? Is
 " AGATCGGA" is optimal? Just because I observed that many reads only
contain part of 3' adapter sequence.
Also, Do I need to trim 5' adapter as well? and How?
Thank so much for your help
Thanh




On Wed, Sep 18, 2013 at 8:12 PM, Jennifer Jackson <j...@bx.psu.edu> wrote:

>  Hi Thanh,
>
> Did the Tuxedo suite not work out for you in the end? Or the other tools
> that Ross suggested? These are both pipelines that are in common use.
> http://lists.bx.psu.edu/pipermail/galaxy-user/2013-July/006367.html
>
> Using a cloud Galaxy and installing tools from the Tool Shed is required
> for certain tools, perhaps that is the problem? Many tools now have
> automatic dependency installation, making set-up much easier. For a
> demonstration, watch the Channel: Galaxy ToolShed videos at Vimeo:
> http://vimeo.com/user20484153
>
> You also may want to look at some of the miRNA specific tools in the Tool
> Shed. They can be found under "Sequence Analysis". Most of these have
> online documentation, or the tool author includes documentation, that you
> can review to see if the tool is a good fit for what you want to do (if it
> is not expression analysis anymore, or you want to try something different
> like DESeq).
> http://toolshed.g2.bx.psu.edu/repository
>
> Hopefully this helps,
>
> Jen
> Galaxy team
>
>
> On 9/18/13 10:19 AM, Hoang, Thanh wrote:
>
> Hi all,
> I would like to analyze my miRNA sequencing analysis from mouse tissue. I
> have not any idea which tools or pipeline work best. Do you have any
> suggestion?
> Regards
> Thanh
>
>
> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org.  Please keep all replies on the list by
> using "reply all" in your mail client.  For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
>   http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>
>   http://galaxyproject.org/search/mailinglists/
>
>
> --
> Jennifer Hillman-Jacksonhttp://galaxyproject.org
>
>
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/

Reply via email to