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

Tophat
by 杨继文 10 Mar '12

10 Mar '12

Dear all, This might be a silly question, but I couldn't figure it out by myself :-((. Could you please tell me how I can find out how many reads have been mapped to the genome after running Tophat for pair end RNA seq data? Thanks in advance. JIwen

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Job running speed is really slow
by 杨继文 10 Mar '12

10 Mar '12

Dear Galaxy team, I found glalaxy (website) is running really slow today. I just did some text manipulations over a very small file. It takes a long time till the gray colour (waiting) turns into yellow (running). Now the jobs are still waiting to be processed (gray colour). I have to analyze my RNA-Seq data next weeks. If the speed continues to be like this, I am sure it is not possible to finish the analysis, since these files are really large. Could you please let me know what I should do to speed it up? Thanks, Jiwen

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Clustal error during Bowtie run (public server)
by Hemarajata, Peera 10 Mar '12

10 Mar '12

Dear all, I was trying to use Bowtie on the public server to align my groomed paired reads to a reference FASTA file. My FASTA contains sequences of 7 contigs (so 7 sequences altogether). After a while this error showed up: Job output not returned by PBS: the output datasets were deleted while the job was running, the job was manually dequeued or there was a cluster error. I re-checked the format of the FASTA file and it looked ok. No illegal character. Would anybody be able to suggest what I can do to fix this? Thank you! Peera Hemarajata, M.D. Advanced graduate student - Versalovic lab Department of Molecular Virology and Microbiology - Baylor College of Medicine Department of Pathology - Texas Children's Hospital Suite 830, 8th Floor Feigin Center. Tel: 832-824-8245

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question from a new Galaxy user
by Elwood Linney, Ph.D. 09 Mar '12

09 Mar '12

[NOTE: I SENT THIS SAME MESSAGE FROM A DIFFERENT EMAIL SERVER NOT CORRESPONDING TO MY USER EMAIL ADDRESS, SO THIS IS A REPEAT EMAIL] Hello: I apologize for bothering you but I am just beginning to work with mRNAseq data and it appears as though Galaxy will be quite useful but I suspect, even after looking some of the tutorials that I will be either making mistakes or just not have a good sense of things. I used "Fetch" off a new Mac computer to ftp 2 datasets yesterday whose sum total memory was over 26gb. It took 5 and one half hours to do that (my login is elwood.linney(a)duke.edu) This morning I had hoped to align this fastq data using your tools. When I identified the two files to put them in the right, history column of galaxy, it appears as though this transfer is taking a long time. Could you give me a time expectation of how long it might take to transfer say a 13gb file into the program if it has already been ftp'd to your site? The unspoken question above is "am I doing something wrong". Sincerely, but naively, Elwood Linney Professor of Molecular Genetics and Microbiology Duke University Medical Center

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Speed up uploading into local Galaxy, terribly slow!!
by Alejandra Rougon 08 Mar '12

08 Mar '12

Hello, I tried to search in the forums and although this question has appeared many times I still don't have a solution. I cannot manage to upload big files into the local galaxy, it just takes ages. Can I not just copy and paste into a local directory? why do I have to upload the files if it is already installed locally? I do not have a server webpage in order to use the url address option If I do it through ftp (locally) what ftp address shall I put? ftp localhost:8080?? Is there any other option to speed up uploading, is so slow that is no longer worth using it, please help me!

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FastQC in main galaxy server?
by Daniel Sobral 08 Mar '12

08 Mar '12

Hi, I've tried FastQC in the main galaxy server and it is throwing me an error: 0 bytes An error occurred running this job: /Traceback (most recent call last): File "/galaxy/home/g2main/galaxy_main/tools/rgenetics/rgFastQC.py", line 149, in <module> assert os.path.isfile(opts.executable),'##rgFastQC.py error - cannot find executable %s' % opts.executable AssertionError: #/ Daniel

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description of "Find diagnostic hits"
by William Hsiao 08 Mar '12

08 Mar '12

Hi, Is there a more detailed explanation on what "Find Diagnostic hits" module in Metagenomic analysis does? Does it take all the hits above user specified cutoffs to one query and return the taxon name if and only if all the hits have the same taxon (my understanding)? Or, does it look at the top few hits or??? Thanks for providing some clarification on the method. Cheers, Will

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Fwd: visualisation of a bam file
by DeQuincy Prescott (UCL) 07 Mar '12

07 Mar '12

Test of forward email. ----------------------------------------------------- DeQuincy Prescott Sen Res Tech to Professor Bhattacharya ----------------------------------- about our group http://tinyurl.com/3264vn ------------------------------------ Mobile: +44 (0) 7590 695 435 Office: +44 (0) 207 608 6951 ----------------------------------------------------- Begin forwarded message: > From: "DeQuincy Prescott (UCL)" <smgxdqc(a)live.ucl.ac.uk> > Subject: visualisation of a bam file > Date: 6 March 2012 19:03:23 GMT > To: <galaxy-user(a)bx.psu.edu> > Cc: Jennifer Jackson <jen(a)bx.psu.edu> > > One of the concerns I am trying to resolve is that I have a bam file which I am trying to visualise on galaxy. > > http://main.g2.bx.psu.edu/u/dqnc/h/unnamed-history > > I was hoping to visualise the data here in Trackster (http://main.g2.bx.psu.edu/visualization/list) > > But it doesn't seem to render. > > I have used "Reference genome build (dbkey): Human Feb. 2009 (GRCh37/hg19) (hg19)" > > But get "no data for this chrom/contig." as a display message. > > The original data is http://qnctv.com/science/chr22hg19.bam (55MB) > > Ultimately we would like to be able to get a VCF file or even better still an essential changes file where known SNPs have been filtered out and any polymorphism have been checked for possible changes to amino acid sequence. > > I am new to Galaxy and still exploring what it can do so correct me if it can't perform what I would like it to do. > > Thank you for any help you can provide. > > ----------------------------------------------------- > DeQuincy Prescott > Sen Res Tech to Professor Bhattacharya > ----------------------------------- > about our group > http://tinyurl.com/3264vn > ------------------------------------ > Mobile: +44 (0) 7590 695 435 > Office: +44 (0) 207 608 6951 > ----------------------------------------------------- >

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question from new Galaxy user
by Elwood Linney 07 Mar '12

07 Mar '12

Hello: I apologize for bothering you but I am just beginning to work with mRNAseq data and it appears as though Galaxy will be quite useful but I suspect, even after looking some of the tutorials that I will be either making mistakes or just not have a good sense of things. I used "Fetch" off a new Mac computer to ftp 2 datasets yesterday whose sum total memory was over 26gb. It took 5 and one half hours to do that (my login is elwood.linney(a)duke.edu) This morning I had hoped to align this fastq data using your tools. When I identified the two files to put them in the right, history column of galaxy, it appears as though this transfer is taking a long time. Could you give me a time expectation of how long it might take to transfer say a 13gb file into the program if it has already been ftp'd to your site? The unspoken question above is "am I doing something wrong". Sincerely, but naively, Elwood Linney Professor of Molecular Genetics and Microbiology Duke University Medical Center

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PE reads d ont map after trimming
by Buxton Chris (NORTH BRISTOL NHS TRUST) 07 Mar '12

07 Mar '12

Hi, I hoped that someone could shed some light onto this . I am attempting to map a set of 2x 150 illumina PE data from a DNA resequencing project. The run had an issue where the quality of the last 50 or so reads of the second run tail off quite considerably. I thought to trim the second read such that the poorer sequence bases are stripped form the end of the read. I attempted to do this using the FASTQ quality trimmer then mapping both reads using bowtie. When I did this however, I went from an alignment of 34% passing filter reads aligned not trimmed (which is not good to start off with), to 0.18%. trim command was set as defaults: Any ideas what I could be doing wrong? ******************************************************************************************************************** This message may contain confidential information. If you are not the intended recipient please inform the sender that you have received the message in error before deleting it. Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Thank you for your co-operation. NHSmail is the secure email and directory service available for all NHS staff in England and Scotland NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients NHSmail provides an email address for your career in the NHS and can be accessed anywhere For more information and to find out how you can switch, visit www.connectingforhealth.nhs.uk/nhsmail ********************************************************************************************************************

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