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
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:
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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 <jen@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:
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
-- Jennifer Hillman-Jacksonhttp://galaxyproject.org
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