---------- Forwarded message ----------
From: shamsher jagat <kanwarjag@gmail.com>o
Date: Mon, May 16, 2011 at 4:19 PM
Subject: problem with filter RNA-seq
To: jeremy.goecks@emory.edu
Cc: galaxy-user@bx.psu.edu

I have tried to follow the steps: File 33 in my history is generated by using filter GTF data by attributes. Two files used were file 29 which is a splicing diff file filtered for yes and file 2 is combined GTF. I used TSS-id for filtering. the out put file file 32 is empty. Any suggestion?

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