Thank Russell for the tip, it was just what i needed. Is there a explanation
of how to construct the instructions for 'Compute' somewhere? I have not been
able to find it.
Also thanks to Hans-Rudolf.
Ian
From: Russell Bell [russell.b...@hci.utah.edu]
S
Hi Dongdong,
The version of TopHat is 1.2.0 and Cufflinks is 1.0.1.
The full list of all Galaxy dependencies can be found on the wiki at:
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies
All the best,
Graham
Dr. Graham Etherington
Bioinformatics Support Officer,
The Sainsbury Laboratory,
Hello,
I was trying to run tophat v1.3.2 on SOLID data and I have this error:
zohra@bart:~/Bureau/cancer$ tophat -o /tmp/tophat_SRR036752/ -g 1 -p 4 -C
/home/zohra/indexes_bowtie/humain_ SRR036752.fastq
[Tue Oct 11 13:23:53 2011] Beginning TopHat run (v1.3.2)
---
Hello,
I am new using Galaxy, I would like ask if it is possible to perform a SNP
and INDEL analysis between two SAM files (mutant and wt) with Galaxy. If so,
could anyone give a hint in how to proceed?
Many thanks for your help in advance,
Kind regards,
Maria G.
___
Hello Ian,
The Compute tool accepts python operator functions. These functions are
applied individually to each line in the input dataset.
In the Compute tool's help (lower portion of the form), simple examples
are shown that demonstrate how the variables c1, c2, etc. will be
interpreted as
Hello Zohra,
For command line (not Galaxy) use of this tool, questions would be best
directed to the tool authors at tophat.cuffli...@gmail.com. That said,
there appears to be a mismatch between the quality scores in your fastq
file and what was expected (integer, linked to the -C option).
S
Hello Maria,
Good tool groups to start with are: "NGS: SAM Tools" and "NGS: Indel
Analysis".
Once you have SNP/Indel the coordinates in BED/Interval format, the
tools in group "Operate on Genomic Intervals" can be used to compare the
two datasets.
Thanks for using Galaxy! Please let us kno
Hi Zohra,
One more bit of help: in the past our team has noticed that Color Space
files from NCBI's SRA database have a "placeholder" adapter base quality
score added in (for an unknown reason).
If you choose to use Galaxy, when passing the file through the FASTQ
Groomer tool (with input and
Thank you for the response.
I can't check my reference genome dataset because I'm using reference
provided by Galaxy (*Mosquito (Anopheles gambiae): AgamP3*). Is there any
solution? Thank you.
--
Chandu
On Mon, Oct 10, 2011 at 7:15 AM, Jeremy Goecks wrote:
>
> Tool execution generated the foll
Is there a plan to add the 69 publicly available genomes from
CompleteGenomics to the SharedData in Galaxy?
http://www.completegenomics.com/sequence-data/download-data/
I am planning to do some analysis of a subset of these genomes in Galaxy
(and I think many more in the future). I also think man
This is a bizarre problem.
The CGI genomes are available on the Bionimbus cloud, but not accessible
through Bionimbus instances. You have to download them and upload them back
into your Bionimbus space. Same for Amazon S3/EC2. This is crazy. CGI uploads
everything to Amazon, and then they send
Hi,
I've been running small tophat jobs as part of a student exercise, but
since yesterday morning (about 7 am CET, or 24 hours ago) my tophat jobs
does not start. Earlier (Monday) jobs started and finished fine. Other
jobs like trimming, getting data from the Main table etc. works.
/D
--
D
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