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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