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.