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

extracting, stitching, converting MAF files: interval_maf_to_merged_fasta.py: command line usage?
by Anton Kratz 20 Jul '12

20 Jul '12

Dear Galaxy team / user mailing list, my question is with respect to command line usage, not about interactive / web-based Galaxy usage. Regarding the publication [1], section "2.3 Stitchers". I want to use the stitcher to extract a given region from MAF files, stitch it together and convert it to FASTA. I downloaded and installed Galaxy according to the instructions from http://wiki.g2.bx.psu.edu/Admin/Get%20Galaxy I believe the actual stitcher is "interval_maf_to_merged_fasta.py" in the /tools/maf directory (not clear from the paper or docs but I belive this is the tool that implements this functionality). How can I actually extract, stitch, convert with interval_maf_to_merged_fasta.py? I have difficulties figuring all necessary command line parameters out by reading the source code. F.e. here I tried to get the stiched FASTA conversion for a region defined in "foo.bed" out of "chr1.maf": $ python ./tools/maf/interval_maf_to_merged_fasta.py -G -i ../foo.bed -m ../chr1.maf -d hg18 -o stdout Traceback (most recent call last): File "./tools/maf/interval_maf_to_merged_fasta.py", line 196, in <module> if __name__ == "__main__": __main__() File "./tools/maf/interval_maf_to_merged_fasta.py", line 107, in __main__ if options.mafSourceType.lower() in ["cached"]: AttributeError: 'NoneType' object has no attribute 'lower' Is it necessary to index the MAF files first somehow? Do I have to set the type of MAF file, and to what? Would be great if someone could give a short overview how to stitch MAF files command-line based. Thank you! Anton References [1] Blankenberg, D., Taylor, J., Nekrutenko, A. & Galaxy Team. Making whole genome multiple alignments usable for biologists. *Bioinformatics (Oxford, England)* *27*, 2426-2428 (2011)

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Error in mapping with bowtie
by Hongkyun Kim 20 Jul '12

20 Jul '12

Hi Experts! I uploaded my data (two pair-end fasq files from illumina), processed with fasq groomer, and then mapped processed data using a reference genome with Bowtie. I got strange errors I cannot possibly understand. None of the files have ind, wped, wsf, or wpf. Any idea? WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'ind': 'module' object has no attribute 'wsf' WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'wped': 'module' object has no attribute 'wsf' WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'wsf': 'module' object has no attribute 'wsf' WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'wpf': 'module' object has no attribute 'wsf' Thanks in advance.

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cuffdiff results missing
by i b 20 Jul '12

20 Jul '12

Hi, I ran cuffdiff using Refseq genes as GTF and two groups of BAM. Group one has two replicates (treated) and group two only one replicate (untreated). When looking at the outputs the following are empty (1 line): TSS group FPKM tracking TSS groups differential expression testing CDS FPKM tracking CDS FPKM differential expression testing CDS overloading diffential expression testing promoters differential expression testing splicing differential expression testing the other four outputs have data downloadable as excel. Is this normal? thanks, ib

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quota limit
by Hongkyun Kim 18 Jul '12

18 Jul '12

Hi there, I am a newbie at Galaxy (registered last night), and have been given 10Gb space. I wonder whether I can increase quota size somehow. I have just uploaded two related files (each 3Gb), and then converted one file to a new format (another 3Gb). Now, I cannot do anything.

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Galaxy intro webinar
by wlathe 18 Jul '12

18 Jul '12

Greetings all! We will be giving a 1 hour 15 minute Intro to Galaxy webinar tomorrow (Thursday, July 19th) at 11am PDT, 2pm EDT. Registration is open and free. Registrants will also have access to a recording, slides and exercises. The webinar will go through the basics of using Galaxy, tools, histories and workflows. If you'd like to attend or would like to see more information, check our our webinar registration page: http://www.openhelix.com/cgi/webinars.cgi Trey (OpenHelix)

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Post
by Rachael Sirois 18 Jul '12

18 Jul '12

rsirois(a)smith.edu

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cuffcompare outputs missing
by i b 18 Jul '12

18 Jul '12

Hi, I ran cuffcompare using 3 samples as inputs (dataset 1-2-3 cufflinks gtf) and a reference annotation (dataset 4). These are the outputs: 5: Cuffcompare on data 1, data 4, and others: transcript accuracy 6: Cuffcompare on data 1, data 4, and others: 1 data tmap file 7: Cuffcompare on data 1, data 4, and others: data 1 refmap file 8: Cuffcompare on data 1, data 4, and others: data 2 tmap file 9: Cuffcompare on data 1, data 4, and others: data 2 refmap file 10: Cuffcompare on data 1, data 4, and others: transcript tracking 11: Cuffcompare on data 1, data 4, and others: combined transcripts my question: why I don't have tmap and refmap on dataset 3?Why only 1 and 2 (arbitrary???) Thanks, ngs-ib

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GCC2012 Registration Deadline
by Dave Clements 17 Jul '12

17 Jul '12

Hello all, This is the final email reminder that the registration deadline for the 2012 Galaxy Community Conference, is at Midnight, Central US time, on Wednesday, July 18. If you aren't registered by the end of Wednesday, you will pay *double* using late/on-site registration. The deadline for booking hotel rooms at the discounted rate has been extended until July 23, or until they fill up (and it looks like they will fill up). The 2012 conference already has more content and more participants than any previous Galaxy meeting. We would love to have you join us. See http://galaxyproject.org/GCC2012 <http://galaxyproject.org/wiki/GCC2012> for details and links. Thanks, Dave C -- http://galaxyproject.org/GCC2012 <http://galaxyproject.org/wiki/GCC2012> http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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UCSC tools
by i b 17 Jul '12

17 Jul '12

Hi, is there a way to create a jobin my history from UCSC genome browser that contains ONLY genes encoding for ONLY cell surface proteins? How can I do that? Thanks a lot! ngs-ib

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(no subject)
by i b 17 Jul '12

17 Jul '12

ok, so if I have 3 different samples I would use 3 different goups and add my samples as replicate within each group. or did you mean to create just one group and add all my 3 samples as 3 replicates within that only group? thanks a lot ngs-ib ________________________________________ From: Jennifer Jackson [jen(a)bx.psu.edu] Sent: Tuesday, July 17, 2012 1:58 AM To: Irene Bassano Cc: galaxy-user(a)lists.bx.psu.edu Subject: Re: [galaxy-user] cuffdiff Hello Irene, On 7/16/12 4:11 PM, Irene Bassano wrote: > Hi, > just few questions about cuffdiff if anyone can answer: > > 1.how can I load more than two sam/bam files?Galaxy gives spaceonly for two files Change the tool form for the option "Perform replicate analysis:" to be "Yes" (the default is "No"). Use two conditions (Groups). > > 2.what to use as input: cufflinks, cuffcompare or cuffmerge? GTF output from any of these may be appropriate. Please see the tutorial on Galaxy main at: http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise FAQ: http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq And the "Common uses" protocols on the Cufflinks web site plus their new paper (also linked at this site, from side bar, as "Protocol"): http://cufflinks.cbcb.umd.edu/tutorial.html Best, Jen Galaxy team > > > Thanks a lot! > > ___________________________________________________________ > 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://galaxyproject.org

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