There is recent paper which has reported summing of FPKM per gene. 
http://genome.cshlp.org/search?fulltext=toung+jm&submit=yes
I have read somewhere that one has to take average FPKM per gene. What is best, 
is not clear as yet.
Intrestingly this paper also suggest 879 milion reads to accurately map 
transcript......
 
Vasu 

--- On Sun, 5/8/11, shamsher jagat <kanwar...@gmail.com> wrote:


From: shamsher jagat <kanwar...@gmail.com>
Subject: Re: [galaxy-dev] question about Filtering Cufflink files
To: galaxy-...@bx.psu.edu
Date: Sunday, May 8, 2011, 10:01 AM




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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