Hi Galaxy users,
I am trying to write a simple tool that sends commands to shell to run Plink (and other analysis packages set up on our Galaxy server). I am new to this, but have managed to write some tools before that work in a similar fashion, at least when you can specify what input and outpu
On Tue, Nov 8, 2011 at 10:26 PM, Austin Paul 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 the
> Bio.SeqI
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
Hello Austin,
You have the correct method to do this all in Galaxy. Use the tool "NGS:
QC and manipulation -> Tabular to FASTQ converter" to do the final step.
Hopefully this helps,
Jen
Galaxy team
On 11/8/11 1:57 PM, Austin Paul wrote:
Hi,
I am curious if anyone knows how to select random
Hello Matthew,
Lucinda is correct, this tool does not interpret the new ID format
correctly. I have opened a bitbucket ticket to track the issue:
https://bitbucket.org/galaxy/galaxy-central/issue/677/update-joiner-tool-to-work-with-casava-18
For now, there is a work-around:
1 - Make certain t
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
i
On Tue, Nov 8, 2011 at 9:57 PM, Austin Paul 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 with
> sequ
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
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The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on t
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 or
I'm having the same issue (though with interlacer). I suspect that
it's an issue with the way the forward and reverse are read. Mine look
like yours, where forward is 1:N and reverse is 2:N instead of the /1
and /2 that the tool says that it expects. Our data are Illumina
pipeline 1.9 (HiSeq), so m
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: fastqsang
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"
Hi!
Does anyone know if it is possible to trim sequencing adaptor sequences away in
Galaxy?
Thanks!
Soetkin Versteyhe, PhD
PostDoc
University of Copenhagen
Faculty of Health Sciences
The Novo Nordisk Foundation
Center for Basic Metabolic Research
Integrative Physiology
Blegdamsvej 3B
2200 Købe
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,
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, Jennife
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:
http://main.g2.bx.psu.edu
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"
mailto: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 it entirely from within
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 tophat.cuffli...@gm
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 ch
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
Senio
Is it possible to limit number of concurrent jobs when job_runner is pbs?
The setting in universe_wsgi.ini is obviously limiting only locally run
jobs.
Petr
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The Galaxy User list should be used for the discussion of
Galaxy analysis and oth
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"
mailto:d.a.matth...@bristol.ac.uk>> wrote:
Hi,
I've had a few email chats with the author of snpEff and the fly in
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 s
Hi Laura,
While the SNPeff developers have made Galaxy wrappers available, this is not a
tool we currently have installed for use on the Galaxy server at
main.g2.bx.psu.edu. Off the top of my head, I don't know of any other public
Galaxy servers that offer this tool, but if you have access to
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.
Hope
Hi Shamsher,
Are you by chance working with more than one open Galaxy browser window
at a time? Doing this is not recommended as it can cause confusing
results between the histories. Instead, move between histories using the
"Options -> Saved Histories" form, in a single browser window.
Plea
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,
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