We are going to add our gene prediction tool to Galaxy Main server, anybody
know whom we should contact?
Hamid Reza Hassanzadeh,
PhD Student & Graduate Research Assistant,
Center for Bioinformatics and Computational Genomics
Joint Georgia Tech and Emory Wallace H Coulter Department of Biomedical
Department of Computer Science at Georgia Institute of Technology
office: KACB 1343
My name is Johnathan Cooper-Knock, I am a clinical fellow based at the
University of Sheffield, UK.
I am trying to use Galaxy for analysis of DNA sequencing data and I have
run into a problem. I am trying to run the SAM/BAM Hybrid Selection Metrics
step on Galaxy (part of the Picard tools) but I can't find bait and target
bed files that Galaxy will accept. My library capture was performed using
the Aglilent All Exon V4 kit and I have uploaded the
'S03723314_Regions.bed' and 'S03723314_Covered.bed' files from '
https://earray.chem.agilent.com/suredesign/search.htm' but Galaxy does not
even seem to recognise them as options for entry. Is this a formatting
issue? Do you know where I can get ready formatted files?
I had fastq.gz files in an Amazon S3 bucket. I created a Galaxy on the Cloud
instance using CloudMan. I used GetData and pasted in the url's of the
fastq.gz files into Galaxy on the Cloud. They were successfully imported
into the session and converted to fastq's, it seems. However, at the next
step (fastq groomer), Galaxy on the Cloud appears to expect that the
imported and converted fastq files are in the same S3 bucket where the
fastq.gz files were. But, they are not there. I read somewhere in
documentation or notes that the data is actually in /mnt/galaxyData folder.
However, I am not sure how to point fastq groomer to this place in the web
interface or alternatively, I am not sure how to move the fastq's back to
the s3 bucket (w/o downloading and re-uploading which would be very
time-consuming). Thanks for any help you can provide.
What you have outlined below is perfect.
I wonder how hard it would be to design a few filters that only look a
certain genes and or filter model organisms out of the dataset.
For example, say you want only data for 16s or only gyrase, but no
/E.coli/ and no /Pseudomanas aeroginosa/
Senior Core Laboratory Research Staff
Advanced Genome Technologies Core
University of Vermont
Vermont Cancer Center
149 Beaumont ave
Health Science Research Facility 303/305
Burlington Vermont 05405
On 9/25/2013 12:06 AM, Jing Yu wrote:
> Hi Scott,
> My first thought is:
> 1. Remove rDNA sequences (and/or other well known highly-conserved
> sequences to reduce the workload in step 2).
> 2. Blast, then remove sequences with > (say 99%) match to > (say 5)
> genus. (Optional if step 1 is already good enough)
> For step 1:
> Build a fasta file of the chosen highly conserved sequences, and
> use it as a feed to blast against your MiSeq result.
> Remove positive hits.
> For step 2:
> Blast remaining MiSeq sequences against NCBI (or whatever) database.
> Remove if it hits more than n genus.
> On 24 Sep 2013, at 22:17, Scott Tighe <scott.tighe(a)uvm.edu
> <mailto:firstname.lastname@example.org>> wrote:
>> Jing et al
>> Thank you for the offer to write some code to help advance the
>> metagenomics arena. It is certainly needed.
>> So the problem is well known with megablast and shotgun metagenomics
>> and without proper understanding and correct software will yield very
>> misleading and in many cases incorrect data. For those of us who wish
>> NOT to move to a protein level of comparison for specific reasons, we
>> are stuck.
>> *The Problem:*
>> If I megablast 50 million sequences from a HiSeq run, millions of
>> rRNA sequences will have a 99% match to all microbes rRNA genbank
>> deposits. Not surprizing since the rRNA is highly conserved. The
>> difference between E.coli and Shigella is 1 to 2 bases for the full
>> 1540 bp 16s. So 16s is not useful for Genus level, and certainly not
>> *So what happens:*
>> The returned matches will have many hits to whatever model organism
>> is in Genbank. For example E coli has 13000 entries for rRNA and
>> Sphearotilus has 3 entries for rRNA. If the blasted sequence matches
>> both, the results will mislead the investigator to think they have
>> 13000 hits to E coli, EVEN if the microbe is Sphearotilus.
>> *The cure?:*
>> If there was a way to filter/ remove all hits ? Let say, for example,
>> that a result has a first match (say E. coli) at >99% a second match
>> (say Pseudomanas) at >99% and a third , forth and fifth match >99 for
>> three other organisms. This sequence _must_ be discarded because it
>> is a conserve sequence.
>> Basically conserved sequence is the enemy and invalidates the entire
>> **Another problem:*
>> If you have a reference sample with 19 non-model microbes, and you
>> run that by HiSeq Shotgun for metagenomics and then megablast, what
>> do you think you get? If E coli is not in the reference sample, how
>> many hits do you think you get? Yes, 10,000 of thousands. So without
>> removing conserved sequences, your data is wrong and you are much
>> better served by culturing and running a Biolog metabolic panel and
>> comparing to the sequence result.
>> So where do we start? I have some shotgun metagenomics data from the
>> reference sample which included the 19 microbes. That was data from a
>> Scott Tighe
>> Senior Core Laboratory Research Staff
>> Advanced Genome Technologies Core
>> University of Vermont
>> Vermont Cancer Center
>> 149 Beaumont ave
>> Health Science Research Facility 303/305
>> Burlington Vermont 05405
>> On 9/20/2013 9:17 PM, Jing Yu wrote:
>>> Hi Scott,
>>> I can do some perl programming, such as local/remote blasting. Can
>>> you specify your problem a little bit clearer, so that maybe I can
>>> write a program to do just that?
>>> 16s is basically useless for identification to genus. Since I
>>> started sequencing 16s in 1992, I have come to realize that without
>>> sequencing the full 1540 bases, it is generally misleading, and
>>> even than, it is not accurate enough to nail genus on more than 1/2
>>> the cases. However, what is your feeling on ITS and gyrase, They
>>> seem to be far more discriminating but those databases have been
>>> decommissioned sometime ago.
>>> The desirable thing would be that Galaxy or NCBI add a "filter
>>> conserved genes" [ ie any hit with a second choice greater than 3%
>>> distance]. Something such as that.
>>> If you (or others) are aware of such a thing, I'd love the here
>>> about it.
I am curious if you could tell me the way that I could add your nglims to my galaxy-dist production system. I have read your step by step procedure here: http://wiki.galaxyproject.org/Admin/Sample%20Tracking/Next%20Gen
but it didn't mention how to add it to the galaxy-dist. Do you have a patch name for it? Should I use hg pull or hg patch? Thanks
I have been mapping my RNA-seq data to mouse genome from a different mouse
strain using TopHat. I am wondering whether TopHat can take SNPs into
account during the alignment? ( using SNPs track as an optional input)?
Dear Galaxy managers,
I would like to ask about the queuing rules for the workflows before
processed on the server?
I use my customized Galaxy workflow which contains 22 following steps
(basically, filtering, trimming and format change of NGS data). I guess the
server is generally very busy during last weeks/months (?), so my job was
waiting about 24 hours in a queue (which would not be a problem), and then
the first step of the workflow was processed, but the following 21 is
again/still waiting (already for another couple of hours...). It makes me
wondering about the queuing rules because I expected that the whole
workflow is queued as one job.. Then my question is if the whole workflow,
once submitted, is listed in the queue, or does the following step queue
only after the previous step is finished (which would mean to wait the
whole queue for each step of the workflow...)?
I routinely used those wrokflows before (months ago) without any
I tried to search similar question in the archive before I posted this
Thanks a lot for your answer,
Zuzana Musilova, PhD.
University of Basel
Vesalgasse 1, CH-4051 Basel
Switzerland - Europe
I have a problem in galaxy to get host/domain name in two different pages.
First one is in the tool installation from toolshed, I got the error below,
The requested URL /admin_toolshed/prepare_for_install was not found on this server.
The second one is in the saved histories. When I click the buttons of the saved histories. I got the similar error like below.
The requested URL /history/list was not found on this server.
I haven't seen these any other pages yet.
My installation is working on LDAP authentication with Proxy. So, I could not find a place to set the domain or host name in these two places that they can actually find the requested URLs.
In the paster.log file. I don't get any error when I install a tool or go to another history. It doesn't report any error.
Thanks for your help,