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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