- galaxy-user - lists.galaxyproject.org

database of known ChIP-seq peaks
by Bogdan Tanasa 27 Sep '13

27 Sep '13

Dear all, please could you recommend any resource/collection/database of known ChIP-seq tracks that also include a significance analysis tool ? thanks, Bogdan

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cleanup_datasets.py with postgresql 8.1
by Malcolm Tobias 27 Sep '13

27 Sep '13

All, My understanding is that the cleanup_datasets.py under scripts/cleanup_datasets should be compatible with 'older' versions of postgresql. I'm running 8.1 under CentOS 5. When I attempt to run the scripts, it fails to clean any data sets. From the logs, I'm noticing messages like: database_connection contains an unknown SQLAlchemy database dialect: postgresql In my universe_wsgi.ini I've defined the database_connection as: database_connection = postgresql://galaxy:********@localhost:5432/galaxydb and am confident it's working as Galaxy works fine, other than this problem with deleting older datasets. The pgcleanup.py script isn't an option, as it requires postgresql >=9.1. I noticed yet another version of cleanup_datasets.py under cron which looks like it might be compatible with postgres, but am leary of trying it as I'm not sure what it means by "1: database directory to clean". I'm not sure what directory to point this to, nor am I confident that just deleting data from the directory is the safest thing. Any suggestions on how to proceed? Thanks! Malcolm -- Malcolm Tobias 314.362.1594

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generating pileup with max depth greater than 8000?
by Lauren Oldfield 26 Sep '13

26 Sep '13

My question: How can I generate a pileup with an output of more than 8000 hits per base? I was generating pileups using the SAM tools --> Generate pileup and do not see an option to change the settings for output. In mpileup there is a variable that looks correct, -D (Output per-sample read depth) , but I cannot figure out how to adjust it. I checked the box, Output per-sample read depth, under the advanced settings but the log file generated still says the max depth was 8000. The pileup files I generated look great but I would like to know what the true read depth is at the 8000 hit plateaus. Any help appreciated. I'm a little out of my depth here. -- Lauren M. Oldfield Hatfull Laboratory Dept. of Biological Sciences University of Pittsburgh 376 Crawford Hall 4249 Fifth Ave Pittsburgh, PA 15260 412-624-6976

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Trying to visualize 2 bam files from Galaxy
by Ben Gift 26 Sep '13

26 Sep '13

I'm trying to start a visualizer with two different files to show a person where the variants are. Can I start IGV or something like it with multiple files? I read the docs and didn't find anything about it. I also asked here http://www.biostars.org/p/82032/

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Variant Annotation in GATK tools
by Yan He 26 Sep '13

26 Sep '13

Hi all, I am analyzing some targeted resequencing data. I was trying to use Variant Annotation tool under GATK after got .VCF file. But some error as following returned. Would you please help me to figure out what happened? Or this tool can only be used for some model organisms? Thanks a lot! "An error occurred with this dataset: Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/space/g2main [Wed Sep 25 03:59:41 EDT 2013] net.sf.picard.sam.CreateSequenceDictionary REFERENCE=/space/g2main/tmp-gatk-4SDjhY/gatk_input.fasta OUTPUT=/space/g2main/tmp-gatk-4SDjhY/dict5123971853428830433.tmp" Yan

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question
by Bondici, Ibi 26 Sep '13

26 Sep '13

On the FastUnifrac webside available at the begining of the year I was able to obtain p-values having “unifrac_env.txt”file, GreenGene Core as the reference tree and “Automatically generate category mapping file” option was previously available. Can I have access to the previous website, rather than the new galaxy? or how can i have the option of "automatically generate catergory file" ? Viorica (Ibi) Bondici PhD. Candidate Department of Food and Bioproduct Sciences College of Agriculture and Bioresources University of Saskatchewan

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Stitch MAF blocks
by Jennifer Di Tommaso 25 Sep '13

25 Sep '13

Hi, I don't undestand how to use the tool "Stitch MAF blocks". I update a small bed file and now I need to run this tool, I don't understand the next step. I'm searching for Novel Linc in some RNA-seq data and I found the lncRscan tool (http://code.google.com/p/lncrscan/wiki/example) and now I have to use "Stitch MAF blocks". The point is: I update the bed file, I select Fetch Alignments -> Stitch MAF blocks, and then I can do nothing, I can only choose among "locally cached alignments" and "alignments in your history". But MAF type/MAF file remain empty, in any case. Can someone be so gentle to solve my problem? Do I need to download a MAF file? Is it normally on Galaxy server, but now it is down? How can I produce a MAF file selecting only some species (29 mammals)? Thank you really much. Jennifer

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Re: [galaxy-user] Metagenomic filtering
by Scott Tighe 25 Sep '13

25 Sep '13

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 Species *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 result. * **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 MiSeq. Scott 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 802-656-2557 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? > > Regards, > Jing > > > > > Gerald > > 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. > > Sincerely > Scott

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de novo RNA-Seq workflow
by Carlos Canchaya 24 Sep '13

24 Sep '13

Hi guys, I am looking for a de novo RNA-seq workflow that uses trinity. Any idea if there is one available? Bests, Carlos Carlos Canchaya ccanchaya(a)gmail.com

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Re: [galaxy-user] History will not load?
by Jennifer Jackson 24 Sep '13

24 Sep '13

Hi Maria, Yes, this is a known issue and we have been working on resolving it today. A red banner is up on the public Main server with a description. That said, from my own testing when you first sent this in to a test I just did now, there appears to be some improvement already. When fully cleared the banner will update. Thank you for your patience, Jen Galaxy team On 9/24/13 6:13 AM, Maria Hoffman wrote: > Hello, > Unfortunately, it appears as though the history will not load again > this AM and the jobs I have set to run last night (cuffdiff) have not > completed either. > Sorry to keep bothering you guys. > > Maria > > > On Mon, Sep 23, 2013 at 2:36 PM, Jennifer Jackson <jen(a)bx.psu.edu > <mailto:jen@bx.psu.edu>> wrote: > > Hello Maria, > > The issue has been resolved. Our apologies for the inconvenience, > > Jen > Galaxy team > > > On 9/22/13 11:55 AM, Maria Hoffman wrote: >> Hello, >> I have been having trouble with Galaxy since yesterday. I have >> been trying to run cuffdiff which has been waiting to run since >> Friday afternoon and now my history will not even load (red error >> message shows up). >> Any incite would be much appreciated. >> Maria >> >> >> ___________________________________________________________ >> The Galaxy User list should be used for the discussion of >> Galaxy analysis and other features on the public server >> atusegalaxy.org <http://usegalaxy.org>. Please keep all replies on the list by >> using "reply all" in your mail client. For discussion of >> local Galaxy instances and the Galaxy source code, please >> use the Galaxy Development list: >> >> http://lists.bx.psu.edu/listinfo/galaxy-dev >> >> To manage your subscriptions to this and other Galaxy lists, >> please use the interface at: >> >> http://lists.bx.psu.edu/ >> >> To search Galaxy mailing lists use the unified search at: >> >> http://galaxyproject.org/search/mailinglists/ > > -- > Jennifer Hillman-Jackson > http://galaxyproject.org > > -- Jennifer Hillman-Jackson http://galaxyproject.org

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