I have shared the history with you Jeremy and has named the files accordingly. I still have same problem and file can not be uploaded to UCSC genome browser
by clicking icon of browser on Galaxy.

Thanks

On Mon, May 9, 2011 at 6:21 AM, Jeremy Goecks <jeremy.goecks@emory.edu> wrote:

(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 <kanwarjag@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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