Re: [galaxy-user] (no subject)

Hello Giuseppe, Please try two things: 1. At the top of the history panel is a small double arrow "refresh" icon. Click this to see if it updates the view. If not, click on the very top "Galaxy" masthead icon. This should not be necessary any longer, but try it anyway. 2. Double check that

[galaxy-user] (no subject)

Hi, I uploaded some file that resulted to be too big and my history showed that that was not more space available. Now I deleted few file, and I should have 80 GB available, but my history shows still that I have no more space available for analysis. Can anyone from the Galaxy team check this f

[galaxy-user] (no subject)

set delivery on ___ 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 discuss

Re: [galaxy-user] (no subject)

Hi Maria, This message indicates that an error occurred on the cluster node processing the job. Normally these are not linked to inputs or tools and the general solution is to re-run the job. Please give this a try today - it is possible the error was linked to recent transient server issues.

[galaxy-user] (no subject)

Hello, I am fairly new to galaxy and I am trying to use bowtie2 to map my reads against a custom genome (specifically a ribosomal RNA fasta file). I have formatted the file as suggested in the Galaxywiki ect and I am still getting the following message: Job output not returned by PBS: the output d

Re: [galaxy-user] (no subject)

Hi Meabh, I'm not familiar with such tools, but maybe you can merge the original files with read-count back to your result file -> "Join two Datasets side by side on a specified field". Cheers, Bjoern > I am new to Galaxy and am using it for analysis of BLAST results and > phylogeny. I have upl

[galaxy-user] (no subject)

I am new to Galaxy and am using it for analysis of BLAST results and phylogeny. I have uploaded a file with contig names, the BLAST GI number, and the total read count for each contig. When I use Galaxy to 'Summarize taxonomy' and 'Draw phylogeny', I have lost the total read counts. Eg. In the r

[galaxy-user] (no subject)

Hello all, The July 2013 Galaxy Update is now available . *Highlights:* - *GCC2013 * starts *today*in Oslo, Norway. - Four new public servers

[galaxy-user] (no subject)

___ 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 Ga

Re: [galaxy-user] (no subject)

Hi Giuseppe, Data has to be local to the instance you are working on in order to use it. You can move individual datasets by downloading/uploading them. And move entire histories using the menu above the history panel and the options "Export to File" and "Import to File". Best, Jen Galaxy t

[galaxy-user] (no subject)

Hi, I have worked so far on the free web-based version of Galaxy; now I have installed Bio-Linux 7, and there is Galaxy in there as well. However, I cannot access to my data (stored on the web version of Galaxy) using Galaxy on Bio Linux. If it is possible, does anyone know how to do it? Thanks,

Re: [galaxy-user] (no subject)

Cuffmerge does some additional steps that Cuffcompare does not; specifically, Cuffmerge attempts to remove assembly artifacts: http://cufflinks.cbcb.umd.edu/manual.html#cuffmerge It's likely that the (presumed) artifacts removed by Cuffmerge account for the differences that you're seeing. Best

[galaxy-user] (no subject)

Dear Galaxy team, I have a question about RNA analysis with the cufflinks package. I have some bam files to analyze from a SOLiD platform. Some previous tests show that these bam/sam files are different from those coming from Tophat and cufflinks cannot assemble them using a reference annotatio

Re: [galaxy-user] (no subject)

Security warning: DO NOT CLICK on the link in this thread. Eric Guo - it is likely that your original sending hotmail email account has been compromised. We have removed it from the galaxy-u...@bx.psu.edu mailing list to prevent further unmoderated posts until the problem is cleared. Contactin

Re: [galaxy-user] (no subject)

Kristis, This data is available further downstream in an RNA-seq analysis pipeline, specifically, as output from the Cuffdiff tool. Take a look at the page for more details: https://main.g2.bx.psu.edu/rna-seq Best, J. On Nov 9, 2012, at 3:42 AM, Vevis, Christis wrote: > Hi, > > I am perfor

[galaxy-user] (no subject)

Hi, I am performing online tophat on 5 different samples which I want to compare for gene expression. Is there any simple way, after the end of tophat for all of them, with which I can have an excel table with the 5 samples and their hits? Something similar to this Vevis1 Vevis2 Vevis3 Vev

[galaxy-user] (no subject)

I am new to the NGS analysis. I need help to solve this problem. As shown in my previous emial/question shown below, I have some paired-end datasets at FASTQ format, and I have problem to split each of these datasets into two datasets (one forward and one reverse). Jennifer instructed me to

[galaxy-user] (no subject)

ok, so if I have 3 different samples I would use 3 different goups and add my samples as replicate within each group. or did you mean to create just one group and add all my 3 samples as 3 replicates within that only group? thanks a lot ngs-ib From: Jenni

Re: [galaxy-user] (no subject)

no longer in the same columns. Is there a way to avoid this shifting? Thanks, Megan From: Jennifer Jackson [j...@bx.psu.edu] Sent: 04 June 2012 22:02 To: Estorninho, Megan Cc: galaxy-user Subject: Re: [galaxy-user] (no subject) Hi Megan, I ran a few tes

Re: [galaxy-user] (no subject)

Hi Megan, I ran a few tests and found that changing the file suffix to .txt when using the "autodetect" upload type function speed up the loading process considerably. As the final result is an identical Galaxy dataset to what is produced with using the existing suffix, this is something I wou

Re: [galaxy-user] (no subject)

Hello Megan, Are you still experiencing problems now? Galaxy may have been busy immediately following the resolution of the cluster problem, although your problem does appear to be unrelated. It sounds like you are uploading file through a browser. A better choice would be to use FTP. This i

[galaxy-user] (no subject)

I have been unable to upload data files into Galaxy Main since Friday 18th May 2012. Today is my fourth day of attempting uploads. Refreshing and leaving the files to upload overnight does not work. Although Jennifer has stated the bug has been fixed at 5.30pm today I am still unable to upload d

[galaxy-user] (no subject)

Hi, I have hit a brick wall when trying to convert wig files from the GEO to bigwig files. Each time I try (and I have tried many times since October), I get the same error. For example, here is a downloaded wig file, that I assigned to the mouse mm8 genome, and the error I got when I tr

[galaxy-user] (no subject)

hi to all Would you please someone help me to remove my email from galaxy users list? Thanks. Moein ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Ple

[galaxy-user] (no subject)

Hi, I read on Readme for MACS that: "For the experiment with several replicates, it is recommended to concatenate several ChIP-seq treatment files into a single file". Now, I have illumina ChipSeq data: two files for IP samples and two files for Control samples. Is It right to use Concatenate datas

[galaxy-user] (no subject)

...Visit and order! I�ve just made an order for 235 $! http://laetitia.servhome.org/com.friend.page.php?wuwid_friend=86ca3 -- Regards Gaurav Thareja ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other fe

[galaxy-user] (no subject)

Hi galaxy I am a new user of galaxy. i met a problem and didnot find similar question in FAQ. I wanted to upload the data from DDBJ DRA dataset to galaxy through UTL method. The file is around 800M. However after uploading, the FASTQ file was just around 2M. So I wanted know whether it is

[galaxy-user] (no subject)

Dear All How can I de-subscribe from the mailing list? Any help would be appreciated Kind Regards M. J ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org.

[galaxy-user] (no subject)

-- Y.P.V.S.Raja Raghava Rao Research Scholar Dr.K.Sreenivasulu Lab Dept.of Animal Sciences School of Life Sciences University of Hyderabad ypvs...@gmail.com 9989733698 ___ The Galaxy User list should be used for the discussion of Galaxy analy

[galaxy-user] (no subject)

-- Y.P.V.S.Raja Raghava Rao Research Scholar Dr.K.Sreenivasulu Lab Dept.of Animal Sciences School of Life Sciences University of Hyderabad ypvs...@gmail.com 9989733698 ___ The Galaxy User list should be used for the discussion of Galaxy analy

[galaxy-user] (no subject)

Hi Jeremy, I tried to run cufflinks to assemble transcripts after running Tophat against my own reference. This error was encountered. What was wrong? How to fix it? Error running cufflinks. [21:01:14] Inspecting reads and determining fragment length distribution. Processed 11130 loci. Warnin

Re: [galaxy-user] (no subject)

Hello Tarek, If you want to reduce the number of identical reads, then please see the tool "FASTA manipulation -> Collapse sequences". Converting formats would be necessary, the tool "Tabular-to-FASTA" can perform this operation. Best, Jen Galaxy team On 8/2/11 3:57 PM, tarek addwebi wrote:

Re: [galaxy-user] (no subject)

On Aug 3, 2011, at 12:49 AM, Addwebi, Tarek wrote: > Hi Dear > Is there anybody whom I can share my data with? I have an important question > that I tried to answer, but I could not. Please see the attachment first, > and let us see the first read in the first row. I need to know how many time

Re: [galaxy-user] (no subject)

sers, Alex Onderwerp: RE: [galaxy-user] (no subject) Hi Alex, Thanks for the email. I will have to have a closer read of the MIRA documentation I think. I know that it definitely makes use of the quality data to some extent, but I hadn't considered whether it ignores low quality data o

Re: [galaxy-user] (no subject)

On Tue, May 24, 2011 at 12:40 AM, Aaron Jex wrote: > Hi, > > Can’t seem to find an answer to this on your wiki site and it’s not in the > tutorial.  I would like to filter my 454 reads for high quality regions, > rename the resulting sequence fragments AND relink the new reads (fragments) > to the

Re: [galaxy-user] (no subject)

amens Aaron Jex Verzonden: dinsdag 24 mei 2011 1:40 Aan: galaxy-u...@bx.psu.edu Onderwerp: [galaxy-user] (no subject) Hi, Can't seem to find an answer to this on your wiki site and it's not in the tutorial. I would like to filter my 454 reads for high quality regions, rename the res

[galaxy-user] (no subject)

Hi, Can't seem to find an answer to this on your wiki site and it's not in the tutorial. I would like to filter my 454 reads for high quality regions, rename the resulting sequence fragments AND relink the new reads (fragments) to the original quality data so that I can take these filtered rea

Re: [galaxy-user] (no subject)

Hello Sreenivas, Did you have a question? Your message arrived without any content other than your content information. Please let us know how we can help, Best, Jen Galaxy team On 4/6/11 6:18 PM, sreenivas kurukuti wrote: -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org _

[galaxy-user] (no subject)

-- Sreenivasulu Kurukuti PhD Department of Animal Sciences School of Life Sciences University of Hyderabad Hyderabad-500 046 A.P., India ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the p

Re: [galaxy-user] (no subject)

Hi Ying, One thing I am concerned is that my files > is kind of large, e.g., for each end I got a file with 20.7 gb, so totally > 41.4 > gb for both ends of this sample. So do you think it is because the files > are too > big? You'll want to use the FTP upload process to upload data this large t

[galaxy-user] (no subject)

Hi: My name is Ying, a postdotoral associate working in Yale university. I am trying to use tophat in galaxy to analyze paired-end RNA-seq data, however, after I groomer and use tophat to analyze them, I only got an empty file. I am wondering what is the problem here. One thing I am concerned is t