April 2012 - galaxy-user - lists.galaxyproject.org

Question about megablast
by shamsher jagat 09 Apr '12

09 Apr '12

I have a question about megablast, I want to megablast my seq: the databases mentioned include (against target databases): htgs27 nt27 wgs 09 phiX174 How can I find details about these databases and which one is human or mouse or may be best for my case. Thanks Vasu

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inconsistency with query results at different time periods
by Jennifer Jackson 09 Apr '12

09 Apr '12

Hello Andigoni, To confirm, the data is being extracted using "Get Data -> UCSC Main" using the Table browser for the hg16 reference genome? If so, I can let you know that the reference genome itself remains the same through time. However, annotation tracks may or may not be updated. Genbank track update frequencies are incremental daily additions and add/remove/change at full releases. From your numbers, it seem like the data is coming from RefSeq Genes. This track was last updated on "2012-04-07". This can be seem at UCSC when browsing the track's description page, the last line of the top section: "Data last updated:". The dates for the corresponding files on their downloads server will also reflect updates (server updated weekly). Unfortunately, there isn't a straightforward way to get back to your prior data unless you have it saved. If you have the exact date of your original data pull, you may be able to reconstruct part of it by mining GenBank directly, but this would be non-trivial and involve your own methods/tools outside of Galaxy. Hopefully this helps to explain the data content. If you have comments or questions about how tracks are processed at UCSC (including this question, they may have a creative solution), their team can be reached at: http://genome.ucsc.edu/contacts.html Going forward, please use our mailing list for questions. Thank you! Jen Galaxy team > ---------- Forwarded message ---------- > From: *andigoni* <andigoni(a)med.auth.gr <mailto:andigoni@med.auth.gr>> > Date: Sun, Apr 8, 2012 at 7:06 PM > Subject: Re: [galaxy-user] inconsistency with query results at different time periods > > Dear Galaxy Gury, > > I would like to ask you a simple question about the human genome > assembly updates. Few months ago I extracted all the introns in bed > format of chromosomes 6,20 and 22 using the hg16 assembly. The total > number of records was 32.050. > > Could you please explain why today the same query results in 32.837 > introns? hg16 isn't a stable release? And how can I go back to the > 32.050 introns in order to process them further? > > > Thank you very much in advance, > Andigoni > > > Andigoni Malousi > Post-doc in Bioinformatics > Aristotle University of Thessaloniki

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MarkupSafe cannot be fetched
by Sarah Maman 06 Apr '12

06 Apr '12

Hi Nate, When I operate on Genomic Intervals → Get Flanks. The user interface for the tool will appear in the center panel. Make sure the dataset 2: UCSC Main... is selected and set Length of Flanking region to 1000 to create intervals 1000bp upstream of each gene. I have this error : Tool execution generated the following error message: WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched The tool produced the following additional output: Skipped 2 invalid lines starting with #40094L "chr5_h2_hap1 281 935 NM_022909 0 + 281 377 0 1 654, 0," Location: Upstream, Region: whole, Flank-length: 1000, Offset: 0 Epilog : job finished at ven avr 6 13:59:08 CEST 2012 Moreover, when I Map with BWA for Illumina ( genome ref and fastq fatsqsanger format ), I have this error : Tool execution generated the following error message: entree dans bwa wapperThe alignment failed. Error aligning sequence. /bin/sh: bwa: command not found WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched The tool produced the following additional output: entree dans bwa for illumina Could not determine BWA version Epilog : job finished at ven avr 6 14:04:13 CEST 2012 Could you please help me ? Thanks in advance, Sarah Maman

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Multiple sample runs using workflow
by Praveen Raj Somarajan 04 Apr '12

04 Apr '12

Hello All, I'm seeking help on how do we run a workflow (say bwa mapping on PE data) on multiple samples (eg: 10 samples, PE data) together. I assume "multiple input files selection" option does not work here as the workflow accepts two fastq input files (PE data). Do you have any experience on this? Best, Raj ________________________________ This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely for the use of the addressee(s). If you are not the intended recipient, please notify the sender by e-mail and delete the original message. Further, you are not to copy, disclose, or distribute this e-mail or its contents to any other person and any such actions that are unlawful. This e-mail may contain viruses. Ocimum Biosolutions has taken every reasonable precaution to minimize this risk, but is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before opening the e-mail or attachment. The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system. OCIMUMBIO SOLUTIONS (P) LTD

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Re: [galaxy-user] Galaxy Server running error in fetching sequences
by Jennifer Jackson 04 Apr '12

04 Apr '12

Hello Hong, To let you know, the Extract tool will work with any fasta dataset in your history as a "Custom reference genome". Instructions are here: http://wiki.g2.bx.psu.edu/Support#Custom_reference_genome Take care, Jen Galaxy team On 4/4/12 10:37 AM, hongxu wrote: > Hi Jen, > > Thank you for the reply. I'll try BED6 and see in Galaxy. > I would also want to try ENSEMBL API, because one of our publication is based on ENSEMBL database. > > Best, > Hong Xu >> From: Jennifer Jackson<jen(a)bx.psu.edu> >> Reply-To: >> To: hongxu<hongxu(a)zju.edu.cn> >> Subject: Re: [galaxy-user] Galaxy Server running error in fetching sequences >> Date: Wed, 04 Apr 2012 07:14:27 -0700 >> >> Hello Hong, >> >> There is likely a problem with the formatting of your input file. BED >> and GFF format are very different, and this may be the problem. You will >> want to input a strict "BED6" file to this tool: >> >> http://wiki.g2.bx.psu.edu/Learn/Datatypes#Bed >> >> http://wiki.g2.bx.psu.edu/Learn/Datatypes#GFF >> >> If you continue to have problems, please submit a bug report by clicking >> on the green bug icon for the red error dataset. This allows us to >> access your data/job privately and provide help/feedback. >> >> Best, >> >> Jen >> Galaxy team >> >>> On Apr 3, 2012, at 4:37 PM, xu hong wrote: >>> >>>> Hi Anton, >>>> >>>> I'm a biological student using Galaxy sever to fetch sequences in >>>> fasta format for our bioinformatics data analysis. First, I uploaded >>>> our BED file(I think there is no significant difference from the GFF >>>> format defined in Galaxy/UCSC), and then use "Fetch Sequences" >>>> function in Galaxy Server. >>>> However, I got the following error: >>>> >>>> "2: Extract Genomic DNA on data 1 >>>> 0 bytes >>>> An error occurred running this job: Traceback (most recent call last): >>>> File "/galaxy/home/g2main/galaxy_main/tools/extract/extract_genomic_dna.py", >>>> line 288, in > >>>> f __name__ == "__main__": __main__() >>>> File "/galaxy/home/g2main/galaxy_main/tools/extract/extract_genomic_dna.py" >>>> " >>>> >>>> Could you help me configure out what's wrong with my analysis or could >>>> you get the fasta file I want for me? >>>> >>>> Attached is the BED file(based on hg18) I uploaded to Galaxy server in psu. >>>> >>>> Thanks. >>>> >>>> Beg your reply. >>>> >>>> Best >>>> Hong Xu >>>> Zhejiang University,China >>>> > >>> >>> >>> ___________________________________________________________ >>> 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] Generating gff file
by Jennifer Jackson 04 Apr '12

04 Apr '12

Hello again, The general path will be: - "Convert Formats -> GFF-to-BED" - click on pencil icon to assign format as "interval", double checking the assignment of the columns, including strand. From there you have different analysis choices, including: * Find out which UCSC tracks have annotation for the gene regions themselves: - "Operate on Genomic Intervals -> Profile Annotations" * Find out which UCSC tracks have annotation for the upstream/downstream regions: - "Operate on Genomic Intervals -> Get flanks" - "Operate on Genomic Intervals -> Profile Annotations" * Extract sequence for the upstream/downstream regions: - "Operate on Genomic Intervals -> Get flanks" - "Fetch Sequences -> Extract Genomic DNA" * Extract complete annotation track from UCSC and find overlapping regions with your regions (any: genes or flanks) - "Get Data -> UCSC Main" select your genome, track of interest (perhaps from profile annotations results, could limit by regions (UCSC accepts up to 1000 regions), etc. - "Operate on Genomic Intervals -> Coverage" this is one suggestion. See our wiki for other choices: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations Hopefully this helps to get you started, Jen Galaxy team On 4/4/12 9:01 AM, Abdullah Al Mahmud wrote: > Hi Jen, > > Thank you for your reply. > I uploaded a gff file to my galaxy. which contains almost 250 gene > annotation. It is for D. melanogaster. I want to know using galaxy and > UCSC genome browser is there a way to collect sequence information > about 1000pb upstream and down stream of all the gene? > > With best regards, > > Abdullah > > On Wed, Apr 4, 2012 at 10:59 AM, Jennifer Jackson<jen(a)bx.psu.edu> wrote: >> Hello Abdullah, >> >> Galaxy can convert BED data to GFF data (type in "GFF" in tool search, top >> of right tool panel). So, any BED file created (MACS, etc.) or imported >> ("Get Data" or other) could be converted and exported as GFF. Please note >> this is "GFF", not "GFF3". >> >> SeqMonk also accepts BED format, so converting may not be necessary. GTF and >> BAM/SAM are also accepted. >> >> Is this what you wanted to know? Did you have a specific data in mind that >> you wanted to create/obtain for visualization? >> >> Please let us know if we can help more, >> >> Jen >> Galaxy team >> >> >> On 4/2/12 12:18 PM, Abdullah Al Mahmud wrote: >>> >>> Hi, >>> >>> Is it possible to generate gff file in galaxy which I can use in Seqmonk? >>> >>> Abdullah >>> >> > > >

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BWA in Galaxy
by shamsher jagat 04 Apr '12

04 Apr '12

Is it possible to align FASTq reads from Illumina Hi-seq reads to human genome in Galaxy? I see only Bowtie/ I guess next question will be how different is Bowtie from BWA? I want to find out sequence variations. Thanks

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Generating gff file
by Abdullah Al Mahmud 04 Apr '12

04 Apr '12

Hi, Is it possible to generate gff file in galaxy which I can use in Seqmonk? Abdullah -- Abdullah Al Mahmud, PhD Postdoctoral fellow University of Montreal Lab of Dr. Jacques Michaud CHU Sainte-Justine Research Center, 3175, Cote-Sainte-Catherine, A-709 Montreal, Quebec, H3T 1C5, Canada. abdullah.al.mahmud(a)umontreal.ca

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Re: [galaxy-user] Galaxy Server running error in fetching sequences
by Anton Nekrutenko 04 Apr '12

04 Apr '12

Hong: I'm forwarding this to our official user mailing list. Please, use it in the future for your inquiries. Thanks! anton Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org On Apr 3, 2012, at 4:37 PM, xu hong wrote: > Hi Anton, > > I'm a biological student using Galaxy sever to fetch sequences in > fasta format for our bioinformatics data analysis. First, I uploaded > our BED file(I think there is no significant difference from the GFF > format defined in Galaxy/UCSC), and then use "Fetch Sequences" > function in Galaxy Server. > However, I got the following error: > > "2: Extract Genomic DNA on data 1 > 0 bytes > An error occurred running this job: Traceback (most recent call last): > File "/galaxy/home/g2main/galaxy_main/tools/extract/extract_genomic_dna.py", > line 288, in <module> > f __name__ == "__main__": __main__() > File "/galaxy/home/g2main/galaxy_main/tools/extract/extract_genomic_dna.py" > " > > Could you help me configure out what's wrong with my analysis or could > you get the fasta file I want for me? > > Attached is the BED file(based on hg18) I uploaded to Galaxy server in psu. > > Thanks. > > Beg your reply. > > Best > Hong Xu > Zhejiang University,China > <IGGPart2.rar>

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Cloudman - Problem starting shared cluster
by mailing list 03 Apr '12

03 Apr '12

Hi guys, After launching Cloudman on the Initial Cluster Configuration dialog I selected the "Share-an-Instance Cluster" option and put in this share string: cm-31bf91279e41769ff78af22c1a276ece/shared/2012-01-12--18-03 But after that I see this message in the log: 12:52:19 - Problem copying shared cluster configuration files. Cannot continue with shared cluster initialization. And nothing else happens after that. The "applications" status stays yellow, and disk status says "0/0". Here is some more information about the run: That sharestring is from a share I made in January. It worked when I last tested it in January. I launched via the BioCloudCentral wep app. Other run information: Instance ID i-8523cee2 Image ID (AMI) ami-500cd139 Security group CloudMan Key pair cloudman_key_pair Placement (zone) us-east-1b Let me know what other information would be helpful. Thanks, Greg

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