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.goe...@emory.edu>wrote:
> (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 <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. >> >> > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ > > >
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