(Starting new thread on galaxy-user.)

Jagat,

It depends what filter tool you're using and what dataset you're filtering. 
There is a generic filter tool that can be used to filter Cuffdiff tabular 
files for either FPKM values and differential expression tests. There is also a 
tool for filtering GTF files based on a Cuffdiff expr dataset. It sounds like 
you may be confusing either the tools or the inputs.

If after double-checking you're still having problems with filtering, please 
put together a short list of your analysis steps and share your history with 
me, and I can take a look.

Thanks,
J.

> Further to my question, It appear that there is some problem with the filter 
> option:
> When I use the isoform/gene exp file as such it work fine but when I filter 
> these files with either parameter such as status if test was successful or on 
> p value it return me empty file. The way am saving the file is - expr file 
> filter save as txt file and upload back in Galaxy.
> Any suggestion?
>  
> Jagat
> 
> 
> On Tue, May 3, 2011 at 3:08 AM, shamsher jagat <kanwar...@gmail.com> wrote:
> Jeremy,
>  
> I have been trying to follow  the steps in filtering Cufflink out put files 
> you have  described in one of the previous messages 
> (http://gmod.827538.n3.nabble.com/Re-downstream-analysis-of-cuffdiff-out-put-td2836457.html):
>  
> I have shared histroy with you, but in summary:
>  
> File 35: when Filter GTF data by attributes value list on data 11 (combined 
> GTF) and data 33 (which is gene expr  file) . Will not this should have one 
> gene per row. But it is not?
> 
> File 39:  Filter GTF file by attribute value list on data 11 and data 38 
> (Cuffdiff splicing expr) it failed. I would assume that it should filter  on 
> the basis of TSSid . The error message is
> 
> Traceback (most recent call last):
>   File 
> "/var/opt/galaxy/g2test/galaxy_test/tools/filters/gff/gtf_filter_by_attribute_values_list.py",
>  line 67, in
>     filter( gff_file, attribute_name, ids_file, output_file )
>   File 
> "/var/opt/galaxy/g2test/galaxy_test/tools/filters/gff/gtf_filter_by_attribute_values_list.py",
>  line 57, in filter
>     if attributes[ attribute_name ] in ids_dict:
> KeyError: 'tss_id'
> 
> 40 : Filter GTF data by attribute list on data 11 and 34 (tss group exp) 
> failed and error message is:
> 
> Traceback (most recent call last):
>   File 
> "/var/opt/galaxy/g2test/galaxy_test/tools/filters/gff/gtf_filter_by_attribute_values_list.py",
>  line 67, in 
>     filter( gff_file, attribute_name, ids_file, output_file )
>   File 
> "/var/opt/galaxy/g2test/galaxy_test/tools/filters/gff/gtf_filter_by_attribute_values_list.py",
>  line 57, in filter
>     if attributes[ attribute_name ] in ids_dict:
> KeyError: 'tss_id'
>  
> I would consider that if one gene has different Id than there is splicing .
> 
> However in contrast isoform file with transcript Id is working fine (File 20)
> 
>  On a different note can I convert GTF file to txt tab delaminated file I 
> tried to convert file 11 in txt (following Edit attributes) but the file is 
> not properly formatted especially col-pid and TSS id. Am I doing something 
> wrong.
> 
> Thanks.
> 
>  
> 
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