Re: [galaxy-user] question about Filtering Cufflink files

[Jeremy Goecks]

Jagat,

First, a couple housekeeping issues:

(a) the questions you're asking are better suited to the galaxy-user list 
(questions about using Galaxy and performing analyses) rather than galaxy-dev 
(questions about installing Galaxy locally and tool development), so I've moved 
this thread to galaxy-user;

(b) please start new threads when appropriate rather than replying to older 
threads as this makes threads shorter and more focused.

Onto your questions:

 I have another question when  I filter gene  list In the filtered list there 
 are multiple rows per gene. I should have one gene per row? I have attached 
 the snap shot of out put, but not sure if galaxy server will take it or not. 
 I did se the discussion on other forum:
 http://seqanswers.com/forums/showthread.php?t=8830

GTF files have multiple lines per feature, so your output is reasonable.


 which suggest that possible complications in getting one gene per row. My 
 next question is in that scenario what should be the best way of representing 
 one gene per FPKM value? should we take average of FPKM per gene? I think in 
 the gene it is till giving the transcript FPKM value but these values are 
 different from previous file filtered with transcript id.

As Vasu noted, this is an ongoing area of research. For some experiments, it 
may be reasonable to group alternatively-spliced isoforms of the same gene and 
jointly estimate FPKM, and for others it may not. Fortunately, if you do want 
to group transcripts to get gene FPKM values, Cuffdiff does this for you: see 
its gene FPKM expression file.

Best,
J.___
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[galaxy-user] Composite Datatypes Q.

[Todd Yilk]

I have a program I'm trying to galaxify that emits a variable number of 
result files. I would like the output of my Galaxy tool to show up in Galaxy as 
an html file with links to the result files. So when you click on the eye, the 
html file should up in the middle pane ... sorry if I'm not describing this in 
an elegant way.

Creating a composite datatype is the way to go in this situation, correct? I'm 
creating a class that inherits from Html. How do I get the result returned from 
my custom generate_primary_file function to show up as a tool's output ... if 
that's the right way to go about this?

Thanks!
___
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[galaxy-user] Filter Tool

[Jeremy Goecks]

(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.
 
  
 
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