Sridhar,

If you read the tool form help text for the differential count tool, you
will have noticed that right at the top, it says:

"Requires a count matrix as a tabular file. These are best made using the
companion HTSeq based counter Galaxy wrapper and your fave gene model to
generate inputs....."

My hope was that anyone reading that hint might realise that
"companion HTSeq based counter Galaxy wrapper" meant they should go take a
look in the same place for something with htseq in the name from the same
author. It seems that I need some assistance to make the wording even more
clear - suggestions will be appreciated.


On Wed, Aug 21, 2013 at 2:37 PM, Sridhar Srinivasan <
sridhar2bioi...@gmail.com> wrote:

> Hi All,
>
> Thanks for the suggestions. I installed the Toolshed ( Differential_Count
> (version 0.21) ). It asks for the input matrix - rows are contigs, columns
> are counts for each sample.
> Any idea on how to generate this matrix file??
>
> Thanks
>
>
> On Tue, Aug 20, 2013 at 12:53 PM, Mahtab Mirmomeni <
> m.mirmom...@student.unimelb.edu.au> wrote:
>
>> Hi Sridhar,
>>
>> I'm using differential_count_model repository by fubar in the test
>> toolshed which has both EdgeR and Deseq2 and it's working for me.
>>
>> Thanks
>>  Mahtab
>>
>>
>> On Tue, Aug 20, 2013 at 5:03 PM, Bjoern Gruening <
>> bjoern.gruen...@gmail.com> wrote:
>>
>>> Hi Sridhar,
>>>
>>> we are developing a DESeq2 tool at the moment, if you want to join get
>>> in touch with me. Its developed here:
>>>
>>> https://github.com/bgruening/galaxytools/tree/master/deseq2
>>>
>>> I will upload our latest progress during the day.
>>> Cheers,
>>> Bjoern
>>>
>>> > Dear users,
>>> >
>>> >
>>> > Could anybody suggest the valid DESeq toolshed for RNA sequencing???
>>> >
>>> >
>>> > Thanks
>>> > Sridhar
>>> >
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>>
>
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-- 
Ross Lazarus MBBS MPH;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444
http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ
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