I would like to use SNPeff for annotation through GATK, However when I upload my file it seems like I cannot use it for this task. My file is .txt and is in this format :
Chr location ref allele alt allele
1 1234567 A T/C
What am I doing wrong?
I like to filter my fastq files (50 bp single end Illumina RNA seq reads) by a maximum threshold (10%) of ambiguous (N) bases.
I can see that the "CLIP" tool removes all reads with one or more N bases.
Is there a way to remove only the reads with five or more N bases using Galaxy?
I think Galaxy was down earlier this week - I saw several several messages
when trying to access the public server, but I'm still getting no function
on the public site. Are there still problems?
I can load the page now, make new workflows and set tasks but no tasks have
been completed in a few days. For example, I set a file to upload yesterday
and it still has the blue working indication. Tasks from two days ago are
grey and "waiting to run".
Any ideas what has gone wrong?
On Fri, Aug 2, 2013 at 12:18 PM, Elizabeth Clare <
> Hi Jen,
> I have had little response from the galaxy public server in the last two
> days (I'm in England) (https://main.g2.bx.psu.edu). At the moment I
> cannot load the webpage or any page associated with it. I have had messages
> "Internal Server Error" then one about a brief shut down saying we should
> contact an administrator if it went on for a while. It appeared to come
> back early this morning but now is unresponsive again.
> I guess I'm reporting a continual error now. Has it gone down?
> Dr. Elizabeth L. Clare
> School of Biological and Chemical Sciences
> Queen Mary University of London
> Mile End Road, London E1 4NS
> Room 1.02, G. E. Fogg Building
> +44 (0)207 882 5687
> "If you say yes more often than you say no, you will do interesting things
> in your life"
Dr. Elizabeth L. Clare
School of Biological and Chemical Sciences
Queen Mary University of London
Mile End Road, London E1 4NS
Room 1.02, G. E. Fogg Building
+44 (0)207 882 5687
"If you say yes more often than you say no, you will do interesting things
in your life"
I haven't used Galaxy for a while, and forgot my password. The problem
with resetting it is that the email I used is no longer active: I graduated.
I need to access the files I uploaded, as its appearing that they did not
collapse in the 'collapse' function properly: I have the same region of a
reference genome mapping to multiple sequences with 100% ID.
Can I please get access to the account? My previous email was:
M.J. Madison-Villar, PhD
Postdoctoral Fellow, Colorado State University
Is it possible to trim a variable number of a specific nucleotide from the
3' ends of fastq RNA reads? The "Manipulate Fastq" utility in Galaxy may
have this ability but I do not know how to create a custom inquiry.
Thanks in advance for any assistance.
For those setups where the server is running on a large, local file system,
is there a method to point Galaxy at a set of files without uploading them
through the web server? This both duplicates the data and (for some
reason) takes a considerable amount of time to upload.
The galaxy stores the output of the job on files/043/dataset_*ID*.dat.
I have two questions here.:
1) Can I find the ID of my output from the Galaxy history? I tried Edit
Attributes, Annotations, tags but couldn't find it.
2) Can I rename my output while initiating the task? If I can how can I do
this and what are the consequences.
Hello Ladies and Gentlemen,
I am Moritz Juchler from University Heidelberg. For my Bachelor thesis I
have to setup Galaxy to find SNP's in genomes from hcc patients. I have a
64-bit openSuse 11.3 server on which I installed Galaxy locally, since we
have a) very large files (>30GB per patient) and b) the data is protection
I have to run this pipeline:
http://www.nature.com/ng/journal/v44/n6/extref/ng.2256-S1.pdf (page 2)
from this paper:
I have in fact some data from exactly these patients, and I want to
reproduce the pipeline as similar as possible. I have this so far:
I would be glad to even do 2-3 steps, I wont need much more for my thesis.
But I find it so hard to find any information about what to do in Galaxy in
The first step in the workflow of the paper I included are the statistics
on page 1 of the supplements, but those aren't necessary (?).
So the first step I have to do after the alignment and the sam to bam
conversion and the dedupe is the first step on page 2 of the supplements:
"Variant calling Tumor"
Which tool in Galaxy do I have to use in order to do this and the following
steps? Any hints, links to papers or answers are welcome :)
How do I process paired reads from an Ilumina Miseq platform? If I first
use "Groomer" and then "Filter by quality", the paired reads get out of
sync. I read some responses to similar questions in this Forum that the
paired reads must first be "joined" before filtering and then split for
mapping. There is also a "Fastq interlacer" command to join reads. However,
I also read in the Forum that Galaxy requires the filtered paired reads to
be of equal length. But would not the filtering process on the joined reads
also modify the length of each differently? Or can the NGS: Picard command
"Paired Read Mate Fixer" be used to re-synchronize the paired reads?
If there is no way around the requirement for equal lengths, then I guess
that it is really not possible to process paired reads in Galaxy? But I am
sure it is just my stupidity.
Full disclosure: Be kind, I am a novice in this field, just learning Galaxy
(which by the way is a fantastic resource!).