Hi,
I use the Galaxy server and was wondering how to use SNPeff tool? I
have seen that it can be integrating with Galaxy on their website
(http://snpeff.sourceforge.net/images/snpEff_galaxy.png) but cannot
see it on the server? Is it something that can be run on the server?
Best Wishes,
Hello Xaingmimg,
When you uncompress the archive locally, does it contain a single file
with more than 5000 reads? The consistent results and even number of
reads (5000) may mean that the archive contains more than one file.
Currently, Galaxy will only load the first file in an archive.
Hi,
I've had a few email chats with the author of snpEff and the fly in the
ointment from my perspective is getting the vcf files it needs through Galaxy.
As I understand it there is no way currently of getting the BAM/SAM files into
the right input format so snpEff can use it within a Galaxy
I got it working just fine on my local server. Could you expand on your vcf
issue? I generate the vcf using gatk.
Sent from my iPhone
On Nov 8, 2011, at 6:36 AM, David Matthews
d.a.matth...@bristol.ac.ukmailto:d.a.matth...@bristol.ac.uk wrote:
Hi,
I've had a few email chats with the author
Hi,
Yes, I see that you can generate the VCF files that way but there is no
seamless way of doing it entirely from within galaxy - i.e. you need to come
out of galaxy at some point (or am I missing something?).
Best Wishes,
David.
__
Dr David A. Matthews
Hello Sheena,
If you concern with using the UCSC version of the database has to do
with the chromosome naming and downstream Cufflinks analysis using
Ensembl's reference GTF files, please see #5 on our FAQ, which
demonstrates how to modify an Ensembl GTF file to be compatible with the
UCSC
Hello Alessia,
This appears to be a known bug in Cuffcompare that can be worked around
by reordering the input files:
http://seqanswers.com/forums/showthread.php?t=5809
If you have questions about this, it would probably be worth asking the
tool authors for input/advice at
Gatk unified genotyper will take a bam/Sam and generate a vcf.
Sent from my iPhone
On Nov 8, 2011, at 6:54 AM, David Matthews
d.a.matth...@bristol.ac.ukmailto:d.a.matth...@bristol.ac.uk wrote:
Hi,
Yes, I see that you can generate the VCF files that way but there is no
seamless way of doing
Hello Lizex,
The primary reason why runs fail is the input data format. A double
check that the reference genome identifiers are the same between the BAM
files and any reference GTF files would be recommended. This and other
common issues are covered in our FAQ here:
Could you direct me how I can save history from a series of steps I have
performed in Galaxy and can later use the same work flow steps. I think
this is what is happening when I logged in back there were two windows open
with my log in info
Thanks
Shamsher
On Tue, Nov 8, 2011 at 5:36 AM,
Hello,
Histories are saved automatically and can be renamed from the active
history panel or Saved history form. To create a Workflow from a
history, use Options - Extract Workflow.
Workflows are covered in the Galaxy 101 tutorial:
http://main.g2.bx.psu.edu/u/aun1/p/galaxy101
Thank you,
Hello Soetkin,
The FASTX-toolkit added into Galaxy has a tool for this. Look under
NGS: QC and manipulation - FASTX-Toolkit for FASTQ data - Clip
adapter sequences.
If this tool does not do exactly what you want, use the Options - Tool
search (top of left tool panel) and enter trim to see
Hi,
I am trying to join two groomed fastq files from a paired-end Illumina
read using the fastq joiner tool. The drop-down menus correctly
identify the groomed fastq files, but after cranking for a few minutes
the tool produces empty output:
FASTQ joiner on data 5 and data 4emptyformat:
Hi,
I am curious if anyone knows how to select random lines from a fastq file.
There is a select random lines tool in text manipulation tools, but it does
not treat fastq files specifically, so it will not group quality lines with
sequence lines. And if I turn the fastq file to tabular form in
Is there an option of running CEAS tool in Galaxy I want to annotate
selected enriched regions of ChIP seq data with gene names etc?
Thanks
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on
On Tue, Nov 8, 2011 at 9:57 PM, Austin Paul austi...@usc.edu wrote:
Hi,
I am curious if anyone knows how to select random lines from a fastq file.
There is a select random lines tool in text manipulation tools, but it does
not treat fastq files specifically, so it will not group quality lines
Hi Peter,
Thanks for the suggestion. For example, I have a fastq file with 50
million reads and I want to randomly select 5 million of them. It seems
biopython would very easily select a single or a handful of reads with the
Bio.SeqIO.index() function. Would it also be able to do the job I am
Hello,
This particular tool group from is not incorporated, but many similar
components exist as tools in Galaxy. In particular, the Operate on
Genomic Intervals - Profile Annotations for a set of genomic intervals
tool may be useful. If not, then importing a gene track (UCSC, ENSEMBL,
etc.)
On Tue, Nov 8, 2011 at 10:26 PM, Austin Paul austi...@usc.edu wrote:
Hi Peter,
Thanks for the suggestion. For example, I have a fastq file with 50 million
reads and I want to randomly select 5 million of them. It seems biopython
would very easily select a single or a handful of reads with
Hi Galaxy users,
I am trying to write a simple tool that sends commands to shell to run Plink (and other analysis packagesset up on ourGalaxy server). I am new to this, but have managed to write some tools before that work in a similar fashion, at leastwhen you can specify what input and output
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