Question: Problem With Filter Rna-Seq
0
gravatar for shamsher jagat
6.9 years ago by
United States
shamsher jagat590 wrote:
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
galaxy • 689 views
ADD COMMENTlink modified 6.9 years ago • written 6.9 years ago by shamsher jagat590
0
gravatar for shamsher jagat
6.9 years ago by
United States
shamsher jagat590 wrote:
Jeremy, I got it working. Thanks 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
ADD COMMENTlink written 6.9 years ago by shamsher jagat590
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