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.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 kanwar...@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-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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