Hi All,

I installed the toolshed htseq_bams_to_count_matrix repository , i gave the
gene model gtf file(ex: tss.gtf file) Gene model (GFF) file to count reads
over from your current history: in this section and all bam files.

it gives error as "
empty
format: tabular, database: hg19
 Traceback (most recent call last): File "/data/galaxy/shed_tools/
testtoolshed.g2.bx.psu.edu/repos/fubar/htseq_bams_to_count_matrix/f69b55c71ae5/htseq_bams_to_count_matrix/htseq_bams_to_count_matrix/htseqsams2mx.py",
line 45, in <module> import HTSeq.scripts.count as htcount "

Thanks




On Wed, Aug 21, 2013 at 10:44 AM, Mahtab Mirmomeni <
m.mirmom...@student.unimelb.edu.au> wrote:

> You can use htseq_bams_to_count_matrix repository by fubar in the test
> toolshed.
>
>
> 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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>>>
>>
>
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