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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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bcf to vcf
by shamsher jagat 07 Aug '12

07 Aug '12

I wasw wondering if there is any option in Glaxy to convert bcf format to vcf format? Thanks Kanwar

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Question about Unified genotyper
by Mathew Bunj 07 Aug '12

07 Aug '12

I have been trying to use either Unified genotyper or Freebayes on one of the Bam file. Both are failing. 1. With Unified genotyper it give me message saying Sequences are not currently available for specified build. I have hg19 related data and using default settings (pick up hg_g1k_v37 no other option). I am not sure why it is giving me this error. 2. As an alternative I tried to run Freebayes with default setting and choosing hg19 - it i snot giving any specific message but undetr bug icon gives me -killed. Now in order to make sure my Bam is OK, I tested out side Galaxy mPile up and with in Galaxy pile up. Any suggestion why UNified genotyper is not working. If needed I can share my history. Thanks.

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Job is waiting to run
by Yan He 07 Aug '12

07 Aug '12

Dear Sir/Madam, I am a registered user of the public Galaxy Server (main). I was trying to upload two files (one is 1.6G and the other is 1.9G) but it was labeled as "Job is waiting to run" forever. Could you please let me know the possible reasons? Sincerely, Yan

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how to use user-defined reference?
by Yan He 07 Aug '12

07 Aug '12

Hi everyone, I am wondering if I can use user-defined reference instead of selecting the reference genome listed in Galaxy while doing mapping. If we can, how can I choose the uploaded reference instead of selecting the reference genome? Any ideas are greatly appreciated! Cheers, Yan

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Fwd: Staring a Cloud Instance
by Mark Lindsay 07 Aug '12

07 Aug '12

Begin forwarded message: > From: Mark Lindsay <m.a.lindsay(a)bath.ac.uk> > Date: 7 August 2012 10:55:03 GMT+01:00 > To: galaxy-user(a)bx.psu.edu > Subject: Staring a Cloud Instance > > I wondered if you might be able to help. > > I have very little computing experience but have been trying to launch a cloud instance for the last 24 hrs. > > Initially I had problems launching the instance in Sahari i.e. it kept saying that it could not connect to the relevant page. > > When I have finally got top the CloudMan launch page it is giving the following message [Critical] Volume 'vol-dd6397db' is located in the wrong availability zone for this instance. You MUST terminate this instance and start a new one in zone 'us-east-1a' > despite the fact that I am sure I have started in zone 'us-east-1a. > > How important are the security codes and keys? > > BW > > Mark > > > > >

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How to block anonymous access and disallow user registration‏
by Joel Rosenberg 06 Aug '12

06 Aug '12

Hello, I've just set up my own instance of Galaxy running in AWS and had a security question that I couldn't find an answer to on the wiki. I'd like to prevent people from hitting my public Amazon IP and using Galaxy. Is there a way to prevent anonymous users from accessing any part of Galaxy except a login prompt and have user registration be invite-only (or perhaps turn it off completely once a handful of accounts have been created)? Thanks, -Joel

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a question about cuffdiff "values"
by Elwood Linney 06 Aug '12

06 Aug '12

Hello: I am a Galaxy-naive molecular, developmental biologist studying repression/derepression of early embryonic gene expression in zebrafish embryos. After attending the Galaxy meeting I returned home and worked up two mRNAseq files to determine RNA expression differences using cuffdiff between a treated and an untreated sample (i.e. data from cuffdiff under the title of "gene differential expression testing"). I downloaded the data, opened it up in an Excel file and captured all the "significant" rows. If I look at the "value 1" and "value 2" columns I find that many of the numbers are single digits. I expect that in one of the columns that the numbers will be very low (that is, less than 1) because the treatment should be inducing gene expression in a subfamily of genes that are repressed. My questions are: 1) what do these numbers represent? 2) If in the "value" column where I expect a higher number has a "value of 10" or less mean anything or should one be selecting for values higher that these single digit numbers 3) And in the column of genes that might be repressed is there really a difference between a "value of 0.1 versus something like 0.01" since that can change my log ratios significantly--this, of course, goes back to my first question I would appreciate any help I could get, sincerely, el linney Professor of Molecular Genetics and Microbiology Duke University Medical Center

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