I have shared the history with you Jeremy and has named the files accordingly. I still have same problem and file can not be uploaded to UCSC genome browser by clicking icon of browser on Galaxy. Thanks On Mon, May 9, 2011 at 6:21 AM, Jeremy Goecks jeremy.goecks@emory.eduwrote:
(Starting new thread on galaxy-user.)
Jagat,
It depends what filter tool you're using and what dataset you're filtering. There is a generic filter tool that can be used to filter Cuffdiff tabular files for either FPKM values and differential expression tests. There is also a tool for filtering GTF files based on a Cuffdiff expr dataset. It sounds like you may be confusing either the tools or the inputs.
If after double-checking you're still having problems with filtering, please put together a short list of your analysis steps and share your history with me, and I can take a look.
Thanks, J.
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.comwrote:
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.
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