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?
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.
Further to my question, It appear that there is some problem with the filter
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.
Hi all ,
I have a set of 1500 sequence obtained from my Chip_Seq experiment. I am interested to Know how many of them are within Conserved non coding Region. My definition of conserved Non coding region is as follows
1. Atleast a 200bp region with 80% conservation between Human , Mice and Chicken
2. Atleast a 200bp region with 70% conservation between Human , Mice , Chicken and Fish
If someone can suggest me how to use galaxy for this purpose.
Thanks in advance.
I am new to Galaxy and am wondering what tools are available for
annotation of SNPs?
I know that snpEff is implemented in Galaxy and this enables annotation
such as location and predicted effect, however I am wondering if there
are any automated means of annotating a polymorphism as known/novel or
determining its frequency in the population.
Does Galaxy offer anything like this or would it be necessary to create
scripts that would for exampole compare to dbSNP for uniqueness and the
1000 genomes project for frequency.
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I am trying to use stat function of Galaxy, and compute q value from p values. it is giving following errors:
An error occurred running this job: Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, :
scan() expected 'a real', got 'pvals'
Please send questions like this to the galaxy-user mailing list, where many people see your email and can help you and/or benefit from it. I've cc'd the list for this reply.
The thread you linked to is out of date. To get sequences for the features in a GTF file, you can use the 'Extract Genomic DNA' tool and set the option 'Interpret features when possible' to Yes. To get sequences for Cufflinks transcripts, use the transcripts.gtf as input to the tool.
On May 12, 2011, at 3:08 AM, Edge Edge wrote:
> I just read through the post at the following link, http://lists.bx.psu.edu/pipermail/galaxy-user/2011-February/001934.html
> I'm facing the same problem as well.
> I'm desired to extract out the assembled transcript by Cufflink.
> Can I know that how I link my output file from Tophat and Cufflink with the Galaxy?
> I'm having the following output file right now:
> Sorry that I got a bit confusing about the explanation that you given to Karen, "in order to get the sequence data for transcripts in a Cuff* GTF file, you'll want to select for only exons (use Galaxy's 'Extract Features' tool) and then use the resultant dataset as input to Extract."
> Thanks a lot for your advice.
> best regards
> Master Student
> UTAR Malaysia
I just read through the post at the following
I'm facing the same problem as well.
I'm desired to extract out the assembled transcript by Cufflink.
Can I know that how I link my output file from Tophat and Cufflink with the
I'm having the following output file right now:
I got a bit confusing about the explanation below:
" in order to get the sequence data for transcripts in a Cuff* GTF file, you'll
want to select for only exons (use Galaxy's 'Extract Features' tool) and then
use the resultant dataset as input to Extract."
Thanks a lot for advice.