Question: Problem With Filter Rna-Seq
0
shamsher jagat • 590 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