Hello, This is a bug and has been fixed. I reran your analyses on our test server and they completed successfully, so you should be good to go. Best, J. On May 3, 2011, at 6:08 AM, shamsher jagat 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-...):

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.

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-... ):

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.