Re: [galaxy-user] Yeast Genome Assembly
Hi Jen,
Could you update the yeast genome to match the following 2011 release?
Ensembl release 9 for Fungal database (which is dependant on SGD database)
[link : http://fungi.ensembl.org/Saccharomyces_cerevisiae/Info/Index].
Thank you,
Edward
On Jun 27, 2011, at 11:58 AM, Jennifer Jackson wrote:
> Hello Edward,
>
> The database Saccharomyces_cerevisiae_S288C_SGD2010 could be considered an
> update (newer release) of the SGD/sacCer2 database, since the source is the
> same - SGD:
> http://www.yeastgenome.org/
>
> UCSC did not update to this newer version of the genome (yet), which is why
> in Galaxy it is not labeled with a UCSC short name (for example, sacCer3).
> If/when UCSC decides to create a sacCer3 genome database, we would very
> likely pull that over or add in the short name to the existing Galaxy genome
> (if they were the same build).
>
> There are advantage with deciding to use either. If using the UCSC genome,
> liftOver would be available as well as the option of viewing at UCSC. But
> using the latest genome from SGD would give you the highest quality assembly
> to work with and viewing in Trackster ("Visualization" at Galaxy is a great
> alternative.
>
> Hopefully this helps,
>
> Jen
> Galaxy team
>
>
> On 6/24/11 8:40 AM, Edward Turk wrote:
>> For yeast analysis I use the following assembly: S. cerevisiae June 2008
>> (SGD/sacCer2) (sacCer2). Recently a new yeast genome has appeared as an
>> option in Galaxy: S. cerevisae str. S288C
>> (Saccharomyces_cerevisiae_S288C_SGD2010). Is this an update to sacCer2?
>> Where is it coming from? I don't see it at UCSC?
>>
>>
>>
>>
>>
>>
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>
> --
> Jennifer Jackson
> http://usegalaxy.org/
> http://galaxyproject.org/
Dr. Edward Turk, Ph.D.
Postdoctoral Fellow
Dep. of Molecular Biology and Microbiology
Case Western Reserve University
School of Medicine, Wood Bldg. W212
10900 Euclid Avenue
Cleveland, OH 44106
440-487-2928
216-368-0385
edwardt...@mac.com
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[galaxy-user] Data changes on usegalaxy.org
Dear Galaxy Users: The usage of our public site is growing exponentially. As a result, we are starting to implement new functionality that will allow users to gauge the size of their datasets and histories. While most changes will be transparent, you may notice some slight change in history behavior stemming from this refactoring process. Here's what you might notice and how deal with it: - Some of the datasets you've previously deleted may be resurrected in your history. Simply re-delete them if you see this happening. - You may also find that necessary metadata files are missing when you use a dataset as a tool input. These metadata files can be regenerated using the "Auto-detect" button on the dataset's "Edit Attributes" page, accessible by clicking the dataset's pencil icon. Thank you for using Galaxy! --nate Galaxy Team http://usegalaxy.org/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at 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/
Re: [galaxy-user] Indel Extraction - Deletion Information
Mike, There actually is not a way to get the deleted base(s) from the SAM alone, since SAM displays only the read and not the reference. Thanks, Kelly On Wed Jun 8, at 4:58 PM, Mike Dufault wrote: Hi All, Does anyone know if there is a way to get the deleted base information that corresponds to the "Extract indels from SAM" output? The output from this tool includes the bases for insertions or "-" for deletions. I want to get the actual bases instead of the "-". I assume there is a way to use the SAM file to extract the information, but if someone already has a nifty way to do it, that would be great. Thanks, Mike ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at 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/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at 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/
Re: [galaxy-user] downloading reference sequences and other questions
Link correction: http://getgalaxy.or/cloud should be http://usegalaxy.org/cloud With the two answers from our team to (hopefully) help, we wish the best for your project, Jen Galaxy team ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at 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/
Re: [galaxy-user] pileup analysis
Dear Andrea: Many apologies for a delay answering this. We are currently in the process of shifting genotyping pipelines to use VCF format, which, combined with a set of VCF manipulation utilities, will make it quite easy to perform operations you request. These should be ready for use by the end of Summer. Thanks for using Galaxy, anton galaxy team Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org On May 18, 2011, at 7:39 PM, Andrea Edwards wrote: > Hello > > I was wondering if there was anything available within galaxy that would let > you do the following with pileup files: > > 1) filter for homozygous SNVs (i.e. that do not contain the reference genome > allele in the genotype) > 2) compare the pileup files for 2 (or more) individuals to find SNVs unique > to each individual and to further limit this to homozygous SNPs unique to > each individual > 3) compare the pileup files for 2 (or more) individuals to find shared SNVs > and to further limit to this to shared SNVs where the individuals have > different alleles (rare as would assume triallelic snv) and then group the > individuals according to the allele for each SNV. > > I could only see the filter pileup tool but nothing for comparing pileup files > > thanks > ___ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at 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/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at 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/
Re: [galaxy-user] downloading reference sequences and other questions
Hello Jo, Please see below On 6/22/11 1:15 PM, Joanne Rampersad wrote: Hi I have a few questions 1. I am trying to use Bowtie to map my data using a reference genome. the genome is available on Galaxy (Escherichia coli DH10B (20079)). Is there a way that I can download the file in fasta format to use as a reference in Tablet? I can import the SAM output into Tablet if I do not give it a reference, but I would like to see it with the reference Galaxy does not currently have genomes available for download. Good sources would be UCSC, NCBI, Ensembl, and other species-specific projects. 2. I have used the Sam to Bam converter and downloaded the file to my computer then tried to import it into Tablet, but it gives an error. Does anyone have any advice on doing this? The best folks to answer Tablet questions would be those tool authors, but that said, a some guesses are that the .bam.bai index file was not loaded along with the .bam? Or maybe the SAM needed to be sorted in some special way first? 3. Does Galaxy have any tools for doing a blast search against a reference genome or database? BLAST is not in on the Galaxy main server, but if you want to see how it is incorporated, it is on our test server (but beware if running any serious jobs, this is an active development area and large runs are not permitted). http://test.g2.bx.psu.edu. After testing out the implementation, and you decide that you want to run BLAST on full datasets using Galaxy, then creating a cloud or local instance is the recommendation. http://getgalaxy.org http://getgalaxy.or/cloud Hopefully this is helpful! Thanks for using Galaxy! Best, Jen Galaxy team Any help/instructions that you point me to is greatly appreciated. Jo ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at 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/ -- Jennifer Jackson http://usegalaxy.org/ http://galaxyproject.org/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at 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/
Re: [galaxy-user] SNP prioritization pipelines
Dear Rad: We do not yet have all necessary tools for making up such as workflow. Thanks for using Galaxy, anton galaxy team Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org On Jun 7, 2011, at 12:07 PM, Radhouane Aniba wrote: > Hi Galaxy users, > > I am new to Galaxy, I am exploring the screencasts over your website, I would > like to know if it is possible to deal with yet unseen example in your > website. > > I downloaded NHGRI GWAS data table and I am interested in a given > traits/complex diseases. > > Is it possible to build a workflow on SNPs prioritization using galaxy ? Does > anyone already did this ? > > Thanks > > Rad > > > ___ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at 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/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at 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/
[galaxy-user] Tophat error
Hi. Newbie here. I'm trying to setup tophat for our local install. I'm getting the following error when I try to run it. Has anyone seen this before or have any ideas what I can try to fix it. Thanks, Simon Error in tophat: [Wed Jun 29 11:54:09 2011] Beginning TopHat run (v1.3.1) --- [Wed Jun 29 11:54:09 2011] Preparing output location ./tophat_out/ [Wed Jun 29 11:54:09 2011] Checking for Bowtie index files [Wed Jun 29 11:54:09 2011] Checking for reference FASTA file Warning: Could not find FASTA file /var/folders/f1/f1aTv8DnERiCv5ic7O3rlk++-+6/-Tmp-/tmpe7Oa0l/dataset_127234.dat.fa [Wed Jun 29 11:54:09 2011] Reconstituting reference FASTA file from Bowtie index Executing: /Volumes/storagepool/oconnorlab/galaxy_dist/bin/bowtie-inspect /var/folders/f1/f1aTv8DnERiCv5ic7O3rlk++-+6/-Tmp-/tmpe7Oa0l/dataset_127234.dat > ./tophat_out/tmp/dataset_127234.dat.fa [Wed Jun 29 11:54:09 2011] Checking for Bowtie Bowtie version: 0.12.5.0 [Wed Jun 29 11:54:09 2011] Checking for Samtools Samtools Version: 0.1.7 [Wed Jun 29 11:54:09 2011] Generating SAM header for /var/folders/f1/f1aTv8DnERiCv5ic7O3rlk++-+6/-Tmp-/tmpe7Oa0l/dataset_127234.dat [Wed Jun 29 11:54:09 2011] Preparing reads format: fastq quality scale: phred33 (default) Left reads: min. length=17, count=2666051 Warning: short reads (<20bp) will make TopHat quite slow and take large amount of memory because they are likely to be mapped to too many places [Wed Jun 29 11:54:27 2011] Mapping left_kept_reads against dataset_127234.dat with Bowtie gzip: stdout: Broken pipe [Wed Jun 29 11:54:27 2011] Processing bowtie hits Traceback (most recent call last): File "/Volumes/storagepool/oconnorlab/galaxy_dist/bin/tophat", line 2607, in sys.exit(main()) File "/Volumes/storagepool/oconnorlab/galaxy_dist/bin/tophat", line 2566, in main user_supplied_deletions) File "/Volumes/storagepool/oconnorlab/galaxy_dist/bin/tophat", line 2256, in spliced_alignment ref_fasta) File "/Volumes/storagepool/oconnorlab/galaxy_dist/bin/tophat", line 2000, in junctions_from_segments if left_reads_map != left_seg_maps[0]: IndexError: list index out of range ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at 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/
Re: [galaxy-user] downloading reference sequences and other questions
Joanne:
1. There is no mechanism for downloading reference sequences from Galaxy at
this time.
2. I am not sure what you mean by 'Tablet'.
3. Megablast tool ('NGS: Mapping -> Megablast') will allow you to perform
comparisons against nt, wgs, and htgs databases.
Thanks for using Galaxy,
anton
galaxy team
Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org
On Jun 22, 2011, at 4:15 PM, Joanne Rampersad wrote:
> Hi
> I have a few questions
>
> 1. I am trying to use Bowtie to map my data using a reference genome.
> the genome is available on Galaxy (Escherichia coli DH10B (20079)). Is
> there a way that I can download the file in fasta format to use as a
> reference in Tablet?
>
> I can import the SAM output into Tablet if I do not give it a
> reference, but I would like to see it with the reference
>
> 2. I have used the Sam to Bam converter and downloaded the file to my
> computer then tried to import it into Tablet, but it gives an error.
> Does anyone have any advice on doing this?
>
> 3. Does Galaxy have any tools for doing a blast search against a
> reference genome or database?
>
> Any help/instructions that you point me to is greatly appreciated.
>
>
> Jo
> ___
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at 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/
___
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Re: [galaxy-user] Error running cufflinks on Galaxy
Thanks Jen, Another problem is with reference-guided assembly. When I produce Cufflinks assembled transcripts files and Cuffcompare combined transcrips file on my own data, it works fine with Galaxy. However, files cannot be visualized in UCSC browser-command "display at UCSC main" produces internal server error. When I try to upload them manually, I receive message "File xxx.gtf' - GFF/GTF group NM_005638 on chrX+, this line is on chrY+, all group members must be on same seq and strand " Any idea on what does it mean and how to fix it? Aleks Quoting Jennifer Jackson : Hello Aleks, Thank you for bring these hg18/hg19 problem to our attention - it was introduced during an edit last week and has now been corrected. The good news is that results are obtained with either - the issue with overlap may be with the Visualization tool itself. When very "zoomed out", the overlap regions can vanish if small enough (we will be correcting/normalizing for this). However, the data is there if you just zoom in, as in the attached screenshot. Hopefully this helps! Best, Jen Galaxy team On 6/24/11 6:19 AM, Aleks Schein wrote: Dear all, I tried to follow the Cufflinks tutorial created by Jeremy. The problems start with first "visualization" step. The is no overlapping at all between Cufflinks transcripts and RefSeq Chr19 reference, provided on the tutorial page. Was that the goal, or transcripts should overlap and something did not work? By the way, mapping for cufflinks was done to hg19, but reference annotation is provided at hg18. Maybe, this is the problem? Aleks Quoting Robert Curtis Hendrickson : Jen, We are running into the same problem on our local install of galaxy. We're running Cufflinks v.1.0.1, on a BAM file (accepted_reads) from TopHat run on mm9 based RNAseq data (paired-end 25mer), and pulled down the changes made to galaxy last month to support the 1.0.1 version of Cufflinks. We (think) we have mm9 indexes locally installed. We can successfully run get_genomic_sequence on mm9 .BED's Turning off bias correction made no difference. We also tried rolling back to Cufflinks v0.9.1 (including the Galaxy patch), and got the same error An error occurred running this job: cufflinks v0.9.1 cufflinks -q --no-update-check -I 50 -F 0.000100 -j 0.000100 -p 4 -N Error running cufflinks. [Errno 2] No such file or directory: 'transcripts.gtf' An error occurred running this job: cufflinks v1.0.1 cufflinks -q --no-update-check -I 50 -F 0.000100 -j 0.000100 -p 4 -N Error running cufflinks. [Errno 2] No such file or directory: 'transcripts.gtf' I can provide a link to the history on our server that you should (theoretically) be able to access. Regards, Curtis -Original Message- From: galaxy-user-boun...@lists.bx.psu.edu [mailto:galaxy-user- boun...@lists.bx.psu.edu] On Behalf Of Jennifer Jackson Sent: Friday, June 10, 2011 3:58 PM To: David Robinson Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] Error running cufflinks on Galaxy Hello David, Cufflinks requires locally cached data to perform the Bias Correction function. Without seeing any sample data, a quick guess is that changing the option "Tool: Cufflinks -> Perform Bias Correction:" from yes to no in that workflow step will probably correct the problem. Another option is to set the dbkey value in the initial input FASTQ file to be a native database (if possible). Hopefully this helps, but if does not correct the problem, please share a history link with data that demonstrates the problem and I can take closer look (emailing link to me directly, to maintain data privacy, would be fine). Jen Galaxy team On 6/8/11 12:07 PM, David Robinson wrote: Hello, When I attempt to run cufflinks based on .sam output from bowtie I get an error: An error occurred running this job: /cufflinks v1.0.1 cufflinks -q --no-update-check -I 30 -F 0.05 -j 0.05 -p 8 -b /galaxy/data/hg19/sam_index/hg19.fa Error running cufflinks. [Errno 2] No such file or directory: 'transcripts.gtf' /What can I do to get around this problem and run cufflinks? My workflow is on http://main.g2.bx.psu.edu and can be found here (I ran it using a .fastq file): http://main.g2.bx.psu.edu/u/dgrtwo/w/cufflinks-workflow-imported-from- uploaded-file Thanks in advance for your help! -David David Robinson Graduate Student Lewis-Sigler Institute for Integrative Genomics Carl Icahn Laboratory Princeton University 646-620-6630 ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at 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:
