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

flaking regions across TSS
by shamsher jagat 29 Jul '12

29 Jul '12

I am interested in getting regions flanking TSS, I am using Glaxaxy and have downloaded TSS sites using this post steps https://lists.soe.ucsc.edu/pipermail/genome/2011-June/026175.html Now what I would like to do is to get 5000 bp upstream an downstream using flank tool in galaxy, but i realize it only gave me option for gene start or whole gene. Is it possible to extract 5000 bp upstream and downstream regions across tss start site . Once I have that then I want to find non overlaping genes in my regions from chipseq data. Thanks Kanwar

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cuffdiff biological replicates
by i b 29 Jul '12

29 Jul '12

Hi guys, a bit of confusion about how to give cuffdiff certain outputs: having 1 control and 8 tumour samples which I consider biological replicates (not technical replicates), how shall give the input to cuffdiff? If I want to use cuffcompare as gtf: shall I cuffcompare all 8samples plus the control and then run cuffdiff using this gtf? When adding the bam files, shall I have to make 8 groups plus control groups? or one groups with 8 bams and second group with the control bam? Much appreciated an answer!! Thanks ib

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cuffdiff: same gene listed with different FPKM values
by i b 28 Jul '12

28 Jul '12

Dear all, has anything like this happened to you? I compared two samples with cuffdiff and when I look at the differentially expressed genes values I have the same gene listed for 5 times with different values. E.g. sample1 sample2 gene 71.6837 9.76435 NM_005514 87.6456 27.3965 NM_005514 115.333 4.81687 NM_005514 38.1879 5.2753 NM_005514 69.4197 5.84387 NM_005514 112.964 3.89226 NM_005514 What does this mean? And how do I know which one represents the real expression level for that gene for the two samples? Thanks, ib

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gene or transcript differential expression testing
by i b 28 Jul '12

28 Jul '12

Hi, I am a bit confused about two outputs of cuffdiff: If I want to see if two samples, e.g. treated and un-treated express similar protein levels, what would be best to look at gene differential expression or transcript diff. expression? Thanks, ib

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metagenomic workflow
by Asuncion Lago 27 Jul '12

27 Jul '12

Hi, I am trying to analyse my eukaryotic metagenome data using yours workflow for windshield splatter analysis. But I find several problems: 1- it is related to "draw phylogeny", this tool fails always for most of my samples, reporting the error: incorrect tree structure. Tree string position 341 2- It is related with the "summarize taxonomy" step. I this case I obtain results but the number of counts are too high compared with the original reads. My samples are small, around 8000 reads and the counts obtained are more that 200000 for some phyla. I guess this is not ok, as far as I understand from your paper than counts are equivalent to reads, am I right? 3- another strange thing is the fact that the number of sequences increase after run the step for select the high quality segments. Any reason for this??? I will really appreciate you help. Thanks in advance Asun

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SAM Tools Pileup
by So, Kathy GZ/US 26 Jul '12

26 Jul '12

Hi, I'm having trouble with the Generate Pileup tool and hope that you could help me troubleshoot this. I ran the tool successfully with the following options: * Use built-in index * Print the mapping quality as the last column * Print all lines * Cap mapping quality = 60 * Call consensus = yes, then default parameters The reference bases of the entire pileup file, however, are all "N." I double checked and the all the files have the same reference genome (mm9). Do you have any ideas on what went wrong? Thanks very much for your help, Kathy Kathy So Genzyme Corp. Functional Genomics 49 New York Ave. Framingham, MA 01701 508-271-4717

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The GATK has a new website and forum
by Geraldine Van der Auwera 26 Jul '12

26 Jul '12

Hi everyone, Just a quick email to let you know that the GATK has a new website and forum. The new website, released in parallel with GATK version 2.0 (beta) features a much improved documentation system and user-friendly introductory materials for new users. Also, the forum is now integrated into the website and linked to the documentation, making it much easier to refer to the docs in forum discussions and find relevant information. If you hated the old Wiki, you're going to love this. http://www.broadinstitute.org/gatk/

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All I want is a question answered please!
by Jennifer Jackson 26 Jul '12

26 Jul '12

Hi Crystal, The galaxy-user(a)galaxy.bx.psu.edu mailing list would be the best for this question. All lists are described here: http://wiki.g2.bx.psu.edu/Support#Mailing_Lists http://wiki.g2.bx.psu.edu/Mailing%20Lists Grey jobs are scheduled to run the and aere in the queue. While they are waiting to run, it is important to not start and restart, as this effectively movest them to the end of the line@ Hopefully this helps, Jen Galaxy team On 7/26/12 8:57 AM, Crystal Marconett wrote: > Hello, > > I am trying desperately to get an answer to a question. I've been over the help area for an hour trying to find an email address to ask questions to, and the only one is the tophat people's email... which is not helpful, because the problem is starting the tool in Galaxy, not getting TopHat errors yet because the job is simply stuck on grey (waiting......) > > The question: > I am trying to start running tophat on my history in the Galaxy main wed interface. I started the job last night at 10pm. It's now 9am. The job is still "waiting to run", ie. grey. How long does it take the Tophat web interface to start? is there a data limit that above which Tophat can no longer run? I don't think this is right, I've run TopHat before on Galaxy with the Illumina whole body tissue data and it took a while, but not this long.... > > My username is: cmarcone(a)usc.edu > the History's name is: Per-RNAseq > The job is : #32, 33, 34, 35 (all grey Tophat for Illumina). > The history has 65.7GB in it, and says it is using 21% (I assume the amount of allocated space left on the server). > > Please help! And if this is not the right e-mail address can you forward this along to the correct one, please!!! or at least let me know the correct email to mail this too. > Thanks! > C -- Jennifer Jackson http://galaxyproject.org

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CloudMan - Can't start nodes
by mailing list 25 Jul '12

25 Jul '12

Hi guys, I created a new Galaxy instance (probably around early July) with the web launcher (https://biocloudcentral.herokuapp.com/launch) I've been coming back and re-using it since then. However for the past week at least I haven't been able to launch new nodes. They show up as red on the indicators, and below I've pasted the error messages. (Could this be related to a new version of cloudman being released?) Thanks, Greg This is the cluster status log from my last attempt: 15:55:02 - Retrieved file 'persistent_data.yaml' from bucket 'cm-[redacted]' to 'pd.yaml'. 15:55:02 - Master starting 15:55:05 - Completed initial cluster configuration. 15:55:25 - Prerequisites OK; starting service 'SGE' 15:55:37 - Configuring SGE... 15:55:37 - Setting up SGE did not go smoothly, running command 'cd /opt/sge; ./inst_sge -m -x -auto /opt/sge/galaxyEC2.conf' returned code '1' and following stderr: '' 15:55:57 - Saved file 'persistent_data.yaml' to bucket 'cm-[redacted]' 15:55:57 - Trouble comparing local (/mnt/cm/post_start_script) and remote (post_start_script) file modified times: [Errno 2] No such file or directory: '/mnt/cm/post_start_script' 15:55:58 - Adding 2 instance(s)... 15:57:32 - Instance 'i-56ba942e' reported alive 15:57:33 - Successfully generated root user's public key. 15:57:33 - Sent master public key to worker instance 'i-56ba942e'. 15:57:47 - Adding instance 'i-56ba942e' as SGE administrative host. 15:57:47 - Process encountered problems adding instance 'i-56ba942e' as administrative host. Process returned code 2 15:57:47 - Adding instance 'i-56ba942e' to SGE execution host list. 15:57:47 - Process encountered problems adding instance 'i-56ba942e' as execution host. Process returned code 2 15:57:47 - Problems updating @allhosts aimed at adding 'i-56ba942e', running command 'export SGE_ROOT=/opt/sge;. $SGE_ROOT/default/common/settings.sh; /opt/sge/bin/lx24-amd64/qconf -Mhgrp /tmp/ah_add_15_57_47' returned code '2' and following stderr: '/bin/sh: 1: .: Can't open /opt/sge/default/common/settings.sh ' 15:57:47 - Waiting on worker instance 'i-56ba942e' to configure itself... 15:57:47 - Instance 'i-54ba942c' reported alive 15:57:47 - Sent master public key to worker instance 'i-54ba942c'. 15:58:01 - Adding instance 'i-54ba942c' as SGE administrative host. 15:58:01 - Process encountered problems adding instance 'i-54ba942c' as administrative host. Process returned code 2 15:58:01 - Adding instance 'i-54ba942c' to SGE execution host list. 15:58:01 - Process encountered problems adding instance 'i-54ba942c' as execution host. Process returned code 2 15:58:01 - Problems updating @allhosts aimed at adding 'i-54ba942c', running command 'export SGE_ROOT=/opt/sge;. $SGE_ROOT/default/common/settings.sh; /opt/sge/bin/lx24-amd64/qconf -Mhgrp /tmp/ah_add_15_58_01' returned code '2' and following stderr: '/bin/sh: 1: .: Can't open /opt/sge/default/common/settings.sh ' 15:58:01 - Waiting on worker instance 'i-54ba942c' to configure itself...

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Re: [galaxy-user] "Jobs is waiting to run" all day on Main
by Lu, Mengmeng 24 Jul '12

24 Jul '12

Same problem here. I want to add a custom build, but it has been processing for more than 5 hours. Is it normal? PS: my reference genome which I used to add the custom build is about 42Mb. Thank you. Mengmeng ----- Original Message ----- From: "Mengmeng Lu" <mira0501(a)neo.tamu.edu> To: "Lee Silver" <lsilver(a)genepeeks.com> Sent: Sunday, July 22, 2012 2:45:52 PM Subject: Re: [galaxy-user] "Jobs is waiting to run" all day on Main Same problem here. I want to add a custom build, but it has been processing for more than 5 hours. Is it normal? PS: my reference genome which I used to add the custom build is about 42Mb. Thank you. Mengmeng ----- Original Message ----- From: "Lee Silver" <lsilver(a)genepeeks.com> To: galaxy-user(a)bx.psu.edu Cc: "Lee Silver" <lsilver(a)genepeeks.com> Sent: Saturday, July 21, 2012 5:20:19 PM Subject: [galaxy-user] "Jobs is waiting to run" all day on Main Since earlier today (at least 6 hours), all of my jobs have been stuck in the "waiting to run" state on the Main Galaxy server. Lee Silver (leemsilver(a)genepeeks.com) ___________________________________________________________ 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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