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 <kanwar...@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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