September 2011 - galaxy-user - lists.galaxyproject.org

trouble Clipping barcodes on data
by KAKOLIE GOSWAMI 12 Sep '11

12 Sep '11

Dear Galaxy Users,I have a data set, for which I'm trying to "Clip" adapter sequences. After splitting the generated data based on different Barcode sequences, I clip the adapter sequences off. This method worked for all the other data sets that I worked with, but seems to act up with one particular data set. I rechecked the sequence and did everything that I could think of to remove this problem, but the error message remains the same as following. Can anyone please help me on this. <http://main.g2.bx.psu.edu/history>##An error occurred running this job: gzip: Segmentation fault stdout: Broken pipe Thanks,Regards Kakolie Goswami Graduate Student

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Re: [galaxy-user] Need help with local install of Galaxy
by Jennifer Jackson 12 Sep '11

12 Sep '11

Hello Aarti, On 9/12/11 1:26 AM, Aarti Desai wrote: > Hi Jennifer, > I have previously used the web version of Galaxy for doing some RNASeq analysis and I loved it! > > I now have some more RNASeq and ChIPSeq data I want to analyze using Galaxy, but the file sizes are more than 2GB and hence am unable to use the web version. Larger data can be loaded onto the public Galaxy main instance at http:/usegalaxy.org using FTP as described: 1 - on the "Get Data -> Upload" tool form, lower section 2 - in this wiki example document http://galaxyproject.org/wiki/Learn/Upload%20via%20FTP 3 - in the screencast example "Tool tutorials -> Using FTP" http://galaxyproject.org/wiki/Screencasts More help can be obtained starting from: http://galaxyproject.org/wiki/Learn > I have got Galaxy installed on a server a couple of weeks back, but have not been able to use it at all. I get stuck at the stage of trying to upload the files. After some time I get an internet connection timeout error. My files are between 3 - 6 Gb in size. Will anybody from your team be able to help with this issue? > > I am sending this directly to you but if you feel this is more appropriate for the mailing list, I will be happy to send it out there, but am getting a little bit desperate trying to get Galaxy to work. You are correct, the mailing list is the best place to ask questions. I will forward this question & reply to the galaxy-user mailing list, as others may encounter similar issues and will benefit from the reply. In the future, using a mailing list to asks questions would be appreciated. http://galaxyproject.org/wiki/Support > Would greatly appreciate your help. > Regards, > Aarti Take care, Jen Galaxy team > > > DISCLAIMER > ========== > This e-mail may contain privileged and confidential information which is the property of Persistent Systems Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Ltd. does not accept any liability for virus infected mails. > > -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support

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Installing Galaxy on my computer
by Lilach F 12 Sep '11

12 Sep '11

Hi, I am a new user of Galaxy. I want to analyze whole human exome data with Galaxy and cannot upload the files (10 Gb each) to the server. Should I install Galaxy on a PC, and work in Unix environment, or there is a more comfortable way? If I should install it - what should be the computer properties, and where can I find the instructions for using it? I found the instructions for installing in Wiki, but didn't find the what computer is should be (RAM, HD, etc). Thanks, Lilach

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Trimming small RNA
by Thiago Mafra 12 Sep '11

12 Sep '11

Hello everybody, I have sequences of small RNA's from 18 to 35nt and accurate trim the sequences of the adapters before aligning the reads with the reference genome. Are there any tools available to it in the Galaxy? Thanks. -- Thiago Mafra Batista Biólogo Molecular Doutorando em Bioinformática - UFMG LGB - ICB/Bloco K4 sala 245 Tel Lab: (31) 3409-2628 CV: http://lattes.cnpq.br/9414909432933240

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Recommended spec for Galaxy server box
by Jerico Nico De Leon Revote 08 Sep '11

08 Sep '11

Hi, What's the recommended base specification for a box for installing the Galaxy server on? Thanks, Jerico

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mpileup tool
by Keith Funkhouser 07 Sep '11

07 Sep '11

Hi all, It seems that the more recent "mpileup" tool that is a part of SAMtools offer better indel prediction than the current "pileup" tool. I've found the following thread http://gmod.827538.n3.nabble.com/samtools-mpileup-update-td3277940.html ...and the following issue https://bitbucket.org/galaxy/galaxy-central/issue/524/implement-wrappers-fo… ...regarding the topic. Is there community demand for this new tool implementation in Galaxy, or is it already in the works? Thanks, Keith Funkhouser

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Chip-Seq, Encode Peaks and Galaxy
by Radhouane Aniba 07 Sep '11

07 Sep '11

Hi everyone, I have a list of genomic regions with some variants and would like to study the correlation between theses variants and epigenomics marks such as histone modifications. >From Encode download page, i got some files corresponding to peaks of these hsitone modifications and would like to know if there is a way to create a pipeline using galaxy to map my variants, depending on genomic regions to the information I have from the histone modification peaks. Is there someone who can point me to a step by step to do things to start using Galaxy ? Thank you Rad

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running cufflinks
by Jennifer Jackson 06 Sep '11

06 Sep '11

===> Please use "Reply All" when responding to this email<=== Hello, File type can be set by using a dataset's pencil icon to reach the "Edit Attributes" form. GTF and GFF are both very similar. It is possible that the 9th field ("group" for GFF, "attributes" for GTF) was not detected automatically upon upload or that there is some problem with format to double check (extra tabs or whitespace). Hopefully this helps, Best, Jen Galaxy team On 9/6/11 1:29 PM, Peng, Tao wrote: > Hi I had 3 GTF files from ensemble, UCSC and NCBI for annotation; ONLY > ensemble were recognized by GALAXY cufflinks as a GTF file although they > all have .GTF. I am NOT sure why UCSC and NCBI GTF files were seen as > GFF files? > > Thx, > > tao -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support

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Extracting reads mapped from bwa mapping
by Austin Paul 06 Sep '11

06 Sep '11

Hello, I recently figured out how to filter the output bwa SAM file for flag type in order to determine the number of reads that were successfully mapped. My question is, I previously thought I could generate a pileup, then sum the number of counts for each base of the reference, and divide this number by the length of the reads (not exact if some reads are hanging over the edge of the reference sequence, but should be close?). But when I compare these methods, I get drastically different results. What am I missing? Thanks, Austin

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Gene Track
by Neal DeLuca 06 Sep '11

06 Sep '11

After using Mac, and clicking on view in Gen Track an error pops up saying: You're seeing this error because you have DEBUG = True in your Django settings file. Change that to False, and Django will display a standard 500 page. How are these setting changed? Neal

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