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.