galaxy-user June 2011

galaxy-user@lists.galaxyproject.org

81 participants
79 discussions

AXT and NIB files for AlignSeq.loc
by John David Osborne 29 Jun '11

29 Jun '11

I was wondering how to get a hold of the axt and/or nib files required by alignseq.loc. It's not mentioned on the local NGA Galaxy setup page. I was surprised to learn that: "Fetch Sequences -> Extract Genomic DNA" requires AXT or NIB alignment files in order to extract mouse genomic DNA from BED file co-ordinates?! I see some AXT files at UCSC (a lot for human) but the alignment file I am guessing I needed (for this mm9 genome extraction) is mouse self? I'm hoping I don't have to generate them all myself, but if I do, I would love to know how to do it (parameters, etc...). Any info appreciated, -John

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Re: [galaxy-user] Cuffdiff Question
by Jeremy Goecks 28 Jun '11

28 Jun '11

Hello Kurinji, > I was at your USC Galaxy seminar last week, which I found very helpful - thank you! Glad to hear that you found the workshop helpful. As a reminder, please email questions about using Galaxy and its tools to the galaxy-user mailing list (which I've cc'd). You may get quicker and different responses from community members, and everyone will benefit from the discussion. > I used my recently generated RNAseq data in Galaxy (which was pre-aligned using tophat and already had cufflinks run on it) - I ran cuffcompare with all the gtf files and then cuffdiff for the three pairs (there is 1 control and 3 different drug treatments - no replicates). I got several output files, as expected, but decided just to look at the gene differential expression as a start. Some questions I have are - > > 1. (very basic question!) which is sample 1 (and corresponding value 1) and sample 2 (and corresponding value 2)in my output file. This is what my output file is called - > > 90: Cuffdiff on data 37, data 38, and data 60: gene differential expression testing 33,969 lines > > Is 37 sample one or sample two? Given the data - I would expect sample 37 to correspond to "value 2" - but I could be wrong. Please let me know! The best way to figure out which dataset corresponds with Cuffdiff's labels is to click the rerun button in the dataset: sample names correspond directly to the reads datasets (i.e. BAM files) provided as input to Cuffdiff. > 2. How do I find the UCSC gene names corresponding with start/end sites - I did input the hg18 UCSC gtf file as a reference You'll need to use a reference annotation (GTF file) that has the gene_name attribute as input for Cufflinks/compare/difff. Typically Ensembl annotations have this attribute; however, you'll need to prepend 'chr' to each line--really, to each chromosome name--in order to bring Ensembl notation in line with UCSC/Galaxy notation. > Actually, I noticed that value 1 in this particular output file is all 0 - no idea why. It is not this way in the other files, making me wonder if there is an error somewhere. I am sure the bam file is okay as I viewed it on IGV and saw the patterns I would expect for some candidate genes I looked at. It's difficult for me to comment without seeing your analysis. Some output files depend on particular attributes being set correctly in the annotation file. You may want to search through our mailing list archives and see if your question has already been answered: http://gmod.827538.n3.nabble.com/Galaxy-Users-f815892.html Good luck, J.

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temporary files
by Christopher Schroeder 28 Jun '11

28 Jun '11

Dear all, we extended the galaxy functionality with a couple of smaller custom scripts. Now we are in the need of some tmpFiles, since our data is getting bigger. As far as I understand galaxy by now there might be several options: - job_working_directory (all "normal" files generated by the job, deleted upon completion of job - safe?) - tmp-folder within the database folder (custom path in universe_wsgi.ini?) - system-tmp-folder (e.g. samtools-wraper -> only very limited space on this harddisk) What is the best way to store temporary data in Galaxy (that can be deleted after job completion)? Thank you in advance for your help! Chris

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Re: [galaxy-user] [galaxy-dev] input security validation
by Roman Valls 28 Jun '11

28 Jun '11

Sorry for the cross-posting, but I guess that's also interesting to Galaxy users... I've been thinking about input validation too... only a bit more generally, on a server/production basis. Nate, on your production setup[1] (galaxy main), do you use any kind of filter or framework a la modsecurity[2] to prevent security issues on third party tools ? How do you mitigate those security risks ? [1] http://usegalaxy.org/production [2] http://modsecurity.org/ On 2011-06-23 00:27, Jennifer Jackson wrote: > Hi Russell, > > Dan Blankenberg is our ChIP-seq expert and will be able to work with you > when he returns from vacation. > > Thank you for your patience! > > Best, > > Jen > Galaxy team > > On 6/20/11 2:22 PM, Russell Bonneville wrote: >> Hello all, >> >> I am Russell, a student working with Dr. Victor Jin at the Dept. of >> Biomedical Informatics, OSU Medical Center. I am developing a Galaxy >> wrapper for our ChIP-seq peak-calling program BELT (PMID: 21138948), and >> I have a question about input validation. Does Galaxy filter for >> malicious field entries (such as XSS attacks) or is this our wrapper’s >> responsibility (the MACS wrapper appears to not perform any explicit >> checks)? Thank you for your time. >> >> Sincerely, Russell Bonneville >> >> >> >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> >> http://lists.bx.psu.edu/ >

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FTP and command line access in Galaxy
by Robert Curtis Hendrickson 28 Jun '11

28 Jun '11

Nate, The Galaxy's ability to pull files with user/password from FTP sites as a client is great. However, I need to pull data from an HTTP site at a sequencing center with user/password (already tried to get them to set up an FTP server, no luck). Any way to do this? If not, would it be easy to add? Regards, Curtis > Hi Nate, > >>> We'd like to set up our local Galaxy to be able to import data (fastq >>> sequences) from an ftp site (with a username/password) into a user's >>> account. Does Galaxy support FTP or would we have to write a wrapper >>> script to do it via HTTP and use the standard data connection methods as >>> described in http://bitbucket.org/galaxy/galaxy-central/wiki/DataSources? >> >> Hi Steve, >> >> You can actually put FTP URLs directly in the URL/paste box on the >> upload form. With a username and password, the format would be: >> >> ftp://user:pass@example.org/path/to/file.ext >> >> I haven't tested that the user/pass bit works, but it should. > >Yep. It works. Thanks for the tip!

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SIFT analysis input and output file
by Charlotte Gueydan 28 Jun '11

28 Jun '11

Sometimes when I do a sift analysis, I noticed that the input and output alleles are different. I don't understand why and what does it means ? could you explain it to me ? For example, here you can see that the input allele is G/A for chr2 (first line) and the output is G/T * input file: chr2 230341630 + G/A chr2 43881517 + A/T chr10 115912482 - G/T chr10 115900918 - C/T * output file: #Chrom Position Strand Allele Codons Transcript ID Protein ID Substitution Region dbSNP ID SNP Type Prediction Score Median Info Num seqs at position User Comment chr2 230341630 + G/T - ENST00000389045 ENSP00000373697 NA EXON CDS rs1803846:A Unknown Not scored NA NA NA chr2 43881517 + A/T ATA-tTA ENST00000260605 ENSP00000260605 I230L EXON CDS rs11556157:T Nonsynonymous TOLERATED 0.47 3.19 7 chr10 115912482 + C/A CGA-CtA ENST00000369285 ENSP00000358291 R179L EXON CDS rs12782946:T Nonsynonymous TOLERATED 0.06 4.32 2 chr10 115900918 + G/A CAA-tAA ENST00000369287 ENSP00000358293 Q271* EXON CDS rs7095762:T Nonsynonymous N/A N/A N/A N/A Regards. Charlotte Gueydan -- *Charlotte Gueydan *, PhD. INSERM/Université Pierre et Marie Curie Hôpital Tenon - bâtiment de recherche 4, rue de la Chine 75020 Paris cedex 20 tel : 01 56 01 83 75

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question on cufflinks output
by Wen Huang 27 Jun '11

27 Jun '11

Dear Galaxy team and users, I have a question on the output by cufflinks on Galaxy. I started with about 28M paired-end reads and mapped them to the reference genome using Tophat on Galaxy. The aligned fragments were assembled by cufflinks, again on Galaxy and I got an output with the first few lines on the bottom of this email. I was wondering how could cufflinks possibly estimate FPKM on the order of e+07 when the coverage is between 8-50 fragments per base and the total mapped fragments smaller than 28M. Assuming that 20M fragments were mapped, the FPKM should be something around coverage/28. Was the e in the output the Euler's number or 10? I appreciate your help. Thanks, Wen Huang tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage status FPKM FPKM_conf_lo FPKM_conf_hi CUFF.2.1 - - CUFF.2 - - chr1:90301-90706 405 21.1837 OK 1.84527e+07 1.10716e+07 2.58338e+07 CUFF.1.1 - - CUFF.1 - - chr1:65419-65692 273 30.9833 OK 2.31848e+07 8.52143e+06 3.78481e+07 CUFF.3.1 - - CUFF.3 - - chr1:135255-135896 641 8.61389 OK 6.31907e+06 3.41968e+06 9.21846e+06 CUFF.4.1 - - CUFF.4 - - chr1:155808-156529 721 7.26147 OK 5.32695e+06 2.88278e+06 7.77112e+06 CUFF.5.1 - - CUFF.5 - - chr1:160421-160729 308 17.6004 OK 1.77483e+07 7.50132e+06 2.79953e+07 CUFF.6.1 - - CUFF.6 - - chr1:170695-171212 517 9.16414 OK 8.41605e+06 4.44869e+06 1.23834e+07 CUFF.7.1 - - CUFF.7 - - chr1:180885-181188 303 30.5702 OK 2.6515e+07 1.36533e+07 3.93767e+07 CUFF.8.1 - - CUFF.8 - - chr1:184397-184702 305 26.712 OK 2.13696e+07 9.94707e+06 3.27921e+07 CUFF.10.1 - - CUFF.10 - - chr1:233237-234095 858 3.71208 OK 3.31435e+06 1.60283e+06 5.02588e+06 CUFF.9.1 - - CUFF.9 - - chr1:203688-204070 382 41.6301 OK 5.36082e+07 4.02061e+07 6.70102e+07 CUFF.11.1 - - CUFF.11 - - chr1:239126-239664 538 19.5995 OK 2.0562e+07 1.45634e+07 2.65605e+07 CUFF.12.1 - - CUFF.12 - - chr1:243903-244327 424 10.3509 OK 1.07542e+07 5.37709e+06 1.61313e+07 CUFF.15.1 - - CUFF.15 - - chr1:240487-240995 508 15.8596 OK 1.83065e+07 1.23671e+07 2.42459e+07

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Unable to load FASTA files?
by Laura Elizabeth Spoor 27 Jun '11

27 Jun '11

Is anyone else having trouble uploading FASTA files to the Galaxy server? I thought it was my files at first, but I have since tried to upload other FASTA files that I have previously had no trouble uploading and I get the same error reported in the info section when I click on the pen icon: Unable to queue job for execution. Resubmitting the job may succeed. (Unfortunately re-submitting the job does not succeed!). The file is 50 MB in size. Any help is greatly appreciated as I am unable to progress my work until this problem is corrected. Best Wishes, Laura -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Error running cufflinks on Galaxy
by Jennifer Jackson 24 Jun '11

24 Jun '11

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

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question on cufflinks output
by Wen Huang 24 Jun '11

24 Jun '11

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galaxy-user June 2011