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

from Galaxy to Megan
by Judith van Bleijswijk 10 Oct '12

10 Oct '12

Dear Galaxy users that also use Megan, I hope you can help me combining Galaxy with Megan4. I followed the Galaxy metagenome workflow (author aun1) on shotgun DNA 454 sequences of two samples that I would like to compare. The results are two nice trees and tables with the lowest taxonomic ranks for the two samples. Besides the taxonomy I am also interested in the functions and I would like to use Megan4 (with SEED and KEGG classification) for this purpose. I tried to import a Galaxy file (.tabular) with c1 =high quality segment name and c2-c13 =blasthit results and a Galaxy fasta file with the high quality segment names and sequences. This does not work and I receive the message parsing failed, no reads found. I am interested to know how you solved this issue and which files in the Galaxy metagenome workflow you use to import into Megan4. Or maybe there is other software that you use to compare suits of functional genes in your metagenome datasets? Regards, Judith van Bleijswijk

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Question about SICER out put
by shamsher jagat 07 Aug '12

07 Aug '12

I used SICR to call peaks and have following out put files: 1. test.1removed bed 2. control1 removed .bed 3. test w 200 graph 4. test w200 normalized graph 5. test w200-G600 FDR.05 island.bed 6. test w200-G600 FDR .05 island filtered.bed 7. test w200-G600 FDR .05 island filtered normalized.wig 8. test w200-G600 FDR.05 score island 9. test w200-G600 summary island Which of these files should be used. I think file 5 and 6 are the ones for visualization as well for annotating with genomic regions. I have read the original paper but it is not very clear what these out puts mean. Could some one please guide me what these files mean and what is useful and rest are intermediate files. My second question is authors of SICER has emphasized about teh importance of choosing gap size and window size. gap size they mention 1-3 -5 depending upon the peak distribution, but I see in Galaxy the default is 600 gap size do we need to change it to 1,2- 5 or I am missing something. Any advise please but I did my searching on net. Thanks

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How to extrapolate differentially expressed genes after running cuffdiff?
by i b 07 Aug '12

07 Aug '12

Hi guys, have a question about the cuffdiff output "differential expression testing". For most of you might sound "naive" but I'm new to this field and I have very little background in statistic. So, I have compared a control sample with 2 biological replicates using cuffdiff. I have now about 4000 genes which were tested. 1. How do I extrapolate the genes which are up- or downregulated from the 4000? 2. Is there a FPKM value above which a gene is up- or downregulated? 3.I used excel and sorted the values from highest to smallest: assuming that control highest value is 200 and the correspondent treated values is 2, can I say that that gene is downregulated in the treated ssamples by a 100 fold chnage? 4. Do I have to use at all the p_values given in the output to extrapolate the most up- or downregualted genes? I do not have yet cummerbund and I am not very good with R. And I 'm lost! Thanks, ib

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reference genome uploading
by i b 07 Aug '12

07 Aug '12

hi, I would like to upload the HPV16 W12E genome (AF125673) (human papilloma virus type 16 ) but I find it hard to be accepted by galaxy. Any suggestion where I can find the correct one? thanks, ib

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Running Cufflinks on Bacterial RNAseq data
by Rachel Krasich 01 Aug '12

01 Aug '12

I am attempting to run Cufflinks on Galaxy main to analyze my E. coli RNAseq data. I have mapped my reads using an outside program (Genious) and uploaded the resulting BAM file. I also have uploaded the E. coli annotations as a gtf file. However when I attempt to run Cufflinks using my annotations it just stays on "Job is waiting to run" for hours. If I click on "Edit attributes", I see an error message "Required metadata values are missing". Does this mean that my files are somehow incomplete and cufflinks will never run, or do I just need to wait longer? When searching around the mailing lists I saw others have had issues with bacteria due to its circular chromosome, and was wondering if this might somehow be related. Thanks. Rachel

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Datasets permanently deleted
by Sarah Maman 01 Aug '12

01 Aug '12

Dear all, In the menu "User" -> "Saved Datasets", all datasets are listed even if some of them have been deleted permanently by deleting its history. So, it's possible to copy an deleted dataset in the current history and that is confusing for users. Do you have any solution to drop these datasets in "saved datasets" ? Thanks in advance, Sarah Maman

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August 2012 Galaxy Update
by Dave Clements 01 Aug '12

01 Aug '12

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Job En-queued, but not running
by Vijaykant N 31 Jul '12

31 Jul '12

Hi, I created a workflow ( https://main.g2.bx.psu.edu/u/vijay-uky/w/rna-seq-analysis ) and uploaded the reference genome (30 MB FASTA file) and the reads (45B FASTQ file after running the FASTQ groomer). Once I ran the workflow on the public server, it will enqueue the needed output (steps) but the job just wouldn't run. I tried to run the same on a local instance at my lab, it works fine. Was curious to know if there is some issue with running tools such as TopHat, Cufflinks and Cuffcompare. If you could let me know, would greatly appreciate. Sincerely, Vijay

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galaxy wiki error
by lufang0411＠sina.com 30 Jul '12

30 Jul '12

Hi I find an error in the galaxy wiki page. please see "Admin/Datatypes/Adding Datatypes" which URL is http://wiki.g2.bx.psu.edu/Admin/Datatypes/Adding%20Datatypes <datatype extension="foo" type="galaxy.datatypes.tabular.Foobar" display_in_upload="true"/><sniffer type="galaxy.datatypes.tabular.Foobar"/> I guess there should be ":" between "tbular" and "Foobar" not "."

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tophat output spice junction output
by i b 30 Jul '12

30 Jul '12

Hi, where can I find an explanation of the columns in the splice junctions output? From 7 to12 they are only numbered thanks, ib

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