min alignement count

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min alignement count

Davide Degli Esposti
Dear Galaxy team,

I am performing a differential expression analysis with a cufflinks-cuffmerge-cuffdiff workflow. I was wondering if the default value of 10 fragments for min alignment count is intended to exclude from the significance test all the loci under 10 counts across all samples or if the counts are 10 for at least one sample the test is performed?

I thank you for your help
Best regards
davide

---
Davide Degli Esposti, PhD
Epigenetic (EGE) Group
International Agency for Research on Cancer
Tel. +33 4 72738036
Fax. +33 4 72738322
150, cours Albert Thomas
69372 Lyon Cedex 08
France 






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Re: min alignement count

Jen Hillman-Jackson
Hi Davide,

I think it it is the first - making it so that both samples in any test would be over this minimum threshold.

Best,

Jen
Galaxy team

On 4/12/13 4:28 AM, Davide Degli Esposti wrote:
Dear Galaxy team,

I am performing a differential expression analysis with a cufflinks-cuffmerge-cuffdiff workflow. I was wondering if the default value of 10 fragments for min alignment count is intended to exclude from the significance test all the loci under 10 counts across all samples or if the counts are 10 for at least one sample the test is performed?

I thank you for your help
Best regards
davide

---
Davide Degli Esposti, PhD
Epigenetic (EGE) Group
International Agency for Research on Cancer
Tel. +33 4 72738036
Fax. +33 4 72738322
150, cours Albert Thomas
69372 Lyon Cedex 08
France 






------------------------------------------------------------------------------------------------
This message and its attachments are strictly confidential. If you are not
the intended recipient of this message, please immediately notify the sender
and delete it. Since its integrity cannot be guaranteed, its content cannot
involve the sender's responsibility. Any misuse, any disclosure or publication
of its content, either whole or partial, is prohibited, exception made of
formally approved use.
------------------------------------------------------------------------------------------------




___________________________________________________________
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-Jackson
Galaxy Support and Training
http://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:

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Jennifer Hillman-Jackson
http://galaxyproject.org