December 2013 - galaxy-user - lists.galaxyproject.org

Help with Summary Statistics
by D. A. Cowart 23 May '14

23 May '14

Hello, I am attempting to use Galaxy to calculate the mean sequence read length and identify the range of read lengths for my 454 data. The data has already been organized and sorted by species. The format of the data is as follows: >HD4AU5D01BHBCQCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC >HD4AU5D01A093MCTCTGTCGCTCTGTCTCTCTTCTCTCTCTCTCTCTCT etc...for each species I have attempted to use the "Summary Statistics" button, however it appears to only be for numerical data and not sequence data. Is this tool/task available via Galaxy? Thank you, Dominique Cowart User name: dac330

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multiplex data
by Ann Holtz-Morris 03 Jan '14

03 Jan '14

Hi, I've several questions regarding multiplex data and its analysis. First, I'm using a MiSeq run on 96-plex (dual index) data. While our current MiSeq data has had the machine the adapters ( including the indexes), it would be nice to be able to clip adapters using a file of adapters rather than one at a time for our older data, which didn't have the adapter clipped. Second, we have the MiSeq run a BWA alignment to the refererence genome for each (96) sample. The folder containing them all averages at about 5GB of data. I noticed that on a local version of Galaxy, a user with administrator privileges can load multiple files. But how can a regular user load them to the main galaxy? I've been reading the developer thread-is this something that will be released soon-ish? Third, Is there a way to run a workflow , several Samtools and Picard analysis, on multiple files so they all get processed? Thanks Ann -- Ann Holtz-Morris, M.S. SRA III de Jong Laboratory CHORI aholtzmorris(a)chori.org

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using SnpEff and SNPSift in Galaxy
by shamsher jagat 02 Jan '14

02 Jan '14

I have a VCF file and I want to filter it for nonsynonymous/ deletion/ insertion seq variations. Once I filter this file and compare between tumor vs normal samples and then annotate such variations. I believe I can filter this file using SnpSift and then can annotate with SnpEff, When I try to use Snsift filter it just says arbitrary expression. Are there rules how to use expression for a particular filter with in galaxy. If any one has used SnpSift in galaxy may share their expertise. Thanks Kanwar

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retaining or reclaiming bed ids
by Gold, Bert (NIH/NCI) [E] 02 Jan '14

02 Jan '14

Hi! Having provided a name (field 4) in a UCSC bed file ( http://www.genome.ucsc.edu/FAQ/FAQformat.html#format1 ) and sought a RefSeq name using the UCSC Table Browser ( http://www.genome.ucsc.edu/cgi-bin/hgTables ), I would now like to recover which line of the bed file delivered which line of the output file… However, I am told I need Galaxy to provide a workflow to do this. Can anyone explain how? eg, one line of my bedfile looks like: chr2 2723752 2723777 seqid6354405 0 - and one line of my intersected table browser output looks like: chr1 176432306 176811970 NM_020318 0 + 176525458 176811590 0 23 248,1835,1072,146,294,193,122,490,129,92,194,147,136,217,172,178,214,169,136,110,72,99,455, 0,92236,131353,207799,226966,228955,232567,235929,239436,243188,246812,248664,276455,276809,302495,306436,307796,326638,328176,330389,336890,377002,379209, Clearly the first line of my bed doesn't correspond to the first line of my intersection output, but as my bed is long, what reference can I use to unambiguously identify which line of output the first line of my intersection corresponds to? How do I do this in Galaxy? PS - I tried this workflow earlier today without success, aiming to achieve a similar objective: https://usegalaxy.org/u/james/w/workflow-from-ucsc-genes-and-symbols PPS- I also note similar issues were raised in this discussion, with Galaxy promoted as the solution, but with no real details about how to achieve the desired results: http://redmine.soe.ucsc.edu/forum/index.php?t=msg&goto=10615&S=0d1b303e6dfd… Bert Gold, Ph.D., FACMG Staff Scientist NCI-Frederick Frederick, MD 21702 VOICE: 301-846-5098 EMAIL: golda(a)mail.nih.gov

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Problems when analyzing my data
by Yitian Xu 02 Jan '14

02 Jan '14

Hi Galaxy, I am a user from Cornell University. And you website is a great help to me and my research. But there are two problems with it I cannot figure out by myself, hoping you can help me. 1. When I uploading the data via FTP, there's option of mouse reference genome mmp10. When I get to Tophat2, there's only mmp9. Is there a problem that I use mmp10 at the beginning and use mmp9 at tophat2? Or maybe you will update the tophat2? 2. I have around 50G space missing. I have one and only one history (at least I can see) with 171.5G, but when I checked my preference I used 225.2G. I don't know where the missing 50G count for then I don't know how to make room for my ongoing analysis. My user name is douyadou. Can you help me check for a min? Thanks. Best, Yitian

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Chrdecoy error in trackster
by doanea＠mskcc.org 02 Jan '14

02 Jan '14

Hello, I’ve been using Galaxy for RNA-seq analysis. Many thanks for this great resource! I have run into a problem that I hope someone might be able to help me with. When loading my .BAM files and/or .gtf files into trackster, I get an error stating: "Input error: Chromosome chrDecoy found in your input file but not in your genome file.” My Illumina fastq files were QCed and aligned using tophat to hg19, and I used cufflinks with hg19 as annotation guide. All my files have hg19 as the dbkey. My guess is that the hg19 I used as a reference differs form the built in model, but I am not sure how I might fix this. Fwiw, I am able to load all my data into IGV, using hg19 as the genome, and visualize everything. Any suggestions would be really appreciated! Thanks! Ashley ===================================================================== Please note that this e-mail and any files transmitted from Memorial Sloan-Kettering Cancer Center may be privileged, confidential, and protected from disclosure under applicable law. If the reader of this message is not the intended recipient, or an employee or agent responsible for delivering this message to the intended recipient, you are hereby notified that any reading, dissemination, distribution, copying, or other use of this communication or any of its attachments is strictly prohibited. If you have received this communication in error, please notify the sender immediately by replying to this message and deleting this message, any attachments, and all copies and backups from your computer.

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Problems with Galaxy 101 Tutorial
by Lance Parsons 02 Jan '14

02 Jan '14

I have a user who is running into some problems on the Galaxy 101 tutorial at: https://usegalaxy.org/u/aun1/p/galaxy101. Specifically, in Safari, it's prompting for a userid and password for each image (and the galaxy account doesn't work). I can confirm this behavior myself. On Chrome, there is no prompt, but no images show up. Any suggestions would be quite welcome. Hoping to give a good first impression... ;-) -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University

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Transferring data to a different account
by Yona Kim 02 Jan '14

02 Jan '14

Hello all, Is there any way in galaxy I can transfer data to a different account? Thanks in advance Yona Kim

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January 2014 Galaxy Update Newsletter
by Dave Clements 31 Dec '13

31 Dec '13

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EdgeR returning empty output
by Anto Praveen Rajkumar Rajamani 19 Dec '13

19 Dec '13

Hi, I have used http://galaxy.nbic.nl/ server to run edgeR on my RNA-seq data to identify differentially expressed genes successfully in August 2013. However, while trying with another digital expression matrix at present, I get only empty output repeatedly. Has anyone used edgeR wrapper recently? What could be the problem? Best wishes, Anto

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GCC2014 Training Day: Topic Nomination is now open
by Dave Clements 18 Dec '13

18 Dec '13

Hello all, Training Day topics are nominated by you <http://bit.ly/gcc2014tdnom>, the Galaxy Community. Please take a minute to nominate a topic. Any topic of interest to the Galaxy Community can be nominated and you are encouraged to nominate more than one topic. If you are looking for ideas, see - what was offered at GCC2013<http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay> , - what topics were nominated in 2013 <http://bit.ly/1i2j1gN>, and - the Events <http://wiki.galaxyproject.org/Events> and the Events Archive<http://wiki.galaxyproject.org/Events/Archive> pages. Nominated topics will be published on the Training Day<http://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> page as they come in. *Nominations close December 20*. Topics will be compiled into a uniform list by the GCC2014 Organizing Committee, and topics will be posted and voted on by the Galaxy Community, January 6-17. Nominate a topic now! <http://bit.ly/gcc2014tdnom> Topics will then be selected and scheduled based on topic interest, and the organizers' ability to confirm instructors for each session. Some very popular sessions may be scheduled more than once. The final schedule will be posted before registration opens. See you in Baltimore! GCC2014 Organizing Committee<http://wiki.galaxyproject.org/Events/GCC2014/Organizers> --- *About GCC2014:* The 2014 Galaxy Community Conference (GCC2014)<http://galaxyproject.org/gcc2014>will be held at the Homewood Campus<http://webapps.jhu.edu/jhuniverse/information_about_hopkins/campuses/homewo…> of Johns Hopkins University <http://jhu.edu/>, inBaltimore, Maryland<http://visitors.baltimorecity.gov/>, United States, from June 30 through July 2, 2014. Galaxy Community Conferences are an opportunity to participate in presentations, discussions, poster sessions, keynotes, lightning talks and bird-of-a-feather gatherings, all about high-throughput biology and the tools that support it. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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Error running CCAT test
by Nicolas Lapalu 18 Dec '13

18 Dec '13

Hi, I tried to run CCAT functionnal test, but I get an exception (same problem via web form) Data are well associated with the hg18 build, which is available in test-data/chrom/hg18.len Error running CCAT. Traceback (most recent call last): File "/home/galaxy-dev/tools/peak_calling/ccat_wrapper.py", line 41, in <module> if __name__ == "__main__": main() File "/home/galaxy-dev/tools/peak_calling/ccat_wrapper.py", line 38, in main return stop_err( tmp_dir, e ) File "/home/galaxy-dev/tools/peak_calling/ccat_wrapper.py", line 13, in stop_err raise exception AssertionError: The required chromosome length file does not exist. Any Idea ? Thanks, Nicolas -- ------------------------------------------------------------------- Nicolas Lapalu INRA - URGI, Bat. 18 Route de Saint Cyr 78000 Versailles Tel: +33 (0)1 30 83 38 10 - Fax: +33 (0)1 30 83 38 99 nicolas.lapalu(a)versailles.inra.fr http://urgi.versailles.inra.fr/ http://www.versailles-grignon.inra.fr/bioger -------------------------------------------------------------------

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problem reimporting histories
by Alessandro Ogier 18 Dec '13

18 Dec '13

Dear galaxy users, here at European Institute of Oncology we're deploying a brand new galaxy install, but facing problems with history (re)importing. We have configured a galaxy running on one node where users took a "sneek peek" on features while developing a real deployment on nfs and cluster integration. Now I have to migrate histories to new galaxy install, I'm doing that on behalf my users because we choose to integrate with an apache proxy that does reverse proxying and ldap authentication. Yesterday I produced four tar.gz for a user, placed on a temporary webserver and then proceeded with reimport on new instance: two where reimported, two not. All those files are relatively small (from 1MB to 13MB), and no clues from galaxy debug log: SUCCESSFUL ONE: galaxy.jobs DEBUG 2013-12-18 13:29:32,718 (354) Working directory for job is: /srv/galaxy/galaxy-dist/database/job_working_directory/000/354 galaxy.jobs.handler DEBUG 2013-12-18 13:29:32,738 (354) Dispatching to local runner galaxy.jobs DEBUG 2013-12-18 13:29:32,826 (354) Persisting job destination (destination id: local) galaxy.jobs.handler INFO 2013-12-18 13:29:32,864 (354) Job dispatched galaxy.jobs.runners.local DEBUG 2013-12-18 13:29:33,151 (354) executing: export GALAXY_SLOTS="1"; python /srv/galaxy/galaxy-dist/lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py http://debian.ieo.eu/drosano/dalia-37.tar.gz /srv/galaxy/galaxy-dist/database/tmp/tmpLAAF5z --url galaxy.jobs DEBUG 2013-12-18 13:29:33,326 (354) Persisting job destination (destination id: local) galaxy.jobs.runners.local DEBUG 2013-12-18 13:29:34,451 execution finished: export GALAXY_SLOTS="1"; python /srv/galaxy/galaxy-dist/lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py http://debian.ieo.eu/drosano/dalia-37.tar.gz /srv/galaxy/galaxy-dist/database/tmp/tmpLAAF5z --url galaxy.jobs DEBUG 2013-12-18 13:29:34,644 job 354 ended galaxy.datatypes.metadata DEBUG 2013-12-18 13:29:34,644 Cleaning up external metadata files UNSUCCESSFUL ONE: galaxy.jobs DEBUG 2013-12-18 13:30:42,824 (392) Working directory for job is: /srv/galaxy/galaxy-dist/database/job_working_directory/000/392 galaxy.jobs.handler DEBUG 2013-12-18 13:30:42,844 (392) Dispatching to local runner galaxy.jobs DEBUG 2013-12-18 13:30:42,934 (392) Persisting job destination (destination id: local) galaxy.jobs.handler INFO 2013-12-18 13:30:42,963 (392) Job dispatched galaxy.jobs.runners.local DEBUG 2013-12-18 13:30:43,236 (392) executing: export GALAXY_SLOTS="1"; python /srv/galaxy/galaxy-dist/lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py http://debian.ieo.eu/drosano/dalia-138.tar.gz /srv/galaxy/galaxy-dist/database/tmp/tmpH8buNE --url galaxy.jobs DEBUG 2013-12-18 13:30:43,400 (392) Persisting job destination (destination id: local) galaxy.jobs.runners.local DEBUG 2013-12-18 13:30:47,524 execution finished: export GALAXY_SLOTS="1"; python /srv/galaxy/galaxy-dist/lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py http://debian.ieo.eu/drosano/dalia-138.tar.gz /srv/galaxy/galaxy-dist/database/tmp/tmpH8buNE --url galaxy.jobs DEBUG 2013-12-18 13:30:47,711 job 392 ended galaxy.datatypes.metadata DEBUG 2013-12-18 13:30:47,712 Cleaning up external metadata files sorry for line wraps, I also attached logs. I cloned your repository on my development machine to try to recreate/debug this issue but unfortunately this time I'm unable to import successfully any history (plain galaxy instance, sqlite, no ext user, no job_conf, either default and stable branches). I'm attaching the new galaxy instance universe_wsgi.ini and job_conf.xml, as you can see they are pretty straight-forward. What I'm asking to you : which is the correct way for debugging this sort of things ? No luck putting some debugging code in * lib/galaxy/tools/actions/history_imp_exp.py * lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py maybe I'm missing something ... also, I'd like to contribute some patch on a couple of minor glitches I found, but I'll write to -dev list for that Thank you, and thanks for this great tool :) ciao -- Alessandro Ogier Specialista Reti e Sistemi - Area Ricerca Direzione ICT Gruppo IEO/CCM Istituto Europeo di Oncologia Via Serio, 15 - 20139 Milan, Italy P +39 02 94375269 M +39 334 6841627 (9am-6am CET) E alessandro.ogier(a)ieo.eu W http://www.ieo.it

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Velvet-galaxy
by Jorge Braun 17 Dec '13

17 Dec '13

Hello mates, I'm new working with velvet and these days have several questions, if anyone knows solution ... It is a great help! Try using the galaxy velvet web platform but there are problems: a) Velveth Velveth and functional? Because galaxy appears when running in error: Unable to run Velveth: No file exists b) there worflow to install velvet in galaxy? thank you very much

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Assembly of Paired and Unpaired sequences
by Prash 16 Dec '13

16 Dec '13

Dear All Greetings! I am analysing a genome of ca. 3.4Mb where I have paired.fa and unpaired.fa files as of now. The sequences have been trimmed before that. Now when I assemble these reads using 'ssake -f paired -g unpaired ...', it takes hell lot of time. Perhaps, I am running out of memory in analyzing the sequence reads. I could use galaxy platform, but would like to stick with ssake. Few questions: What if I concatenate these two files, would I be able to peruse this for blasting against my reference? At this point, how do I know whether or not paired or single-end reads are better? How do I know the two chromosomal sequences? Help appreciated for stupid questions :) Thank you in advance Prash Prashanth Suravajhala, PhD. Homepage: http://www.bioinformatics.org/wiki/Prash Linkedin: http://dk.linkedin.com/in/prashbio <http://dk.linkedin.com/in/prashbio> “What counts in life is not the mere fact that we have lived. It is what difference we have made to the lives of others that will determine the significance of the life we lead.” — Nelson Mandela On 15 December 2013 18:00, <galaxy-user-request(a)lists.bx.psu.edu> wrote: > Send galaxy-user mailing list submissions to > galaxy-user(a)lists.bx.psu.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.bx.psu.edu/listinfo/galaxy-user > or, via email, send a message with subject or body 'help' to > galaxy-user-request(a)lists.bx.psu.edu > > You can reach the person managing the list at > galaxy-user-owner(a)lists.bx.psu.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of galaxy-user digest..." > > > HEY! This is important! If you reply to a thread in a digest, please > 1. Change the subject of your response from "Galaxy-user Digest Vol ..." > to the original subject for the thread. > 2. Strip out everything else in the digest that is not part of the thread > you are responding to. > > Why? > 1. This will keep the subject meaningful. People will have some idea from > the subject line if they should read it or not. > 2. Not doing this greatly increases the number of emails that match search > queries, but that aren't actually informative. > > Today's Topics: > > 1. Re: fastqc and blast? trinity? (Peter Cock) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 14 Dec 2013 21:18:29 +0000 > From: Peter Cock <p.j.a.cock(a)googlemail.com> > To: Jorge Braun <braun_bio(a)hotmail.com> > Cc: "galaxy-user(a)lists.bx.psu.edu" <galaxy-user(a)lists.bx.psu.edu> > Subject: Re: [galaxy-user] fastqc and blast? trinity? > Message-ID: > <CAKVJ-_4BKUgtb37EYF_FsAAj= > YC+eT5ZuRvFgZk0pUySKdmsxg(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > On Sat, Dec 14, 2013 at 8:52 AM, Jorge Braun <braun_bio(a)hotmail.com> > wrote: > > > > Hello, of course, Jennifer is right for the first question . For > > the second question about blast ... I wonder if running after > > blast in galaxy I can remove sequences that can contaminate > > the data. It's possible? > > > > The BLAST suite is not available on the public Galaxy > server at http://usegalaxy.org but is available from the > Galaxy Tool Shed if you have a local Galaxy instance: > > http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/ > > One way to filter your FASTA file based on BLAST hits > would be to use the tabular output from BLAST with > this sequence filtering tool: > > http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id > > e.g. If you want to remove transcripts which seem > to be mitochondria, you could BLAST against a > mitochondrial database, and take only the sequence > with no hits. > > Regards, > > Peter > > > ------------------------------ > > _______________________________________________ > galaxy-user mailing list > galaxy-user(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-user > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > > End of galaxy-user Digest, Vol 90, Issue 13 > ******************************************* >

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fastqc and blast?
by Jorge Braun 16 Dec '13

16 Dec '13

Hello mates, I have two doubts galaxy: a) I have rna-seq data from Illumina and do fastqc ... the results are good but when I fastgroomer to Sanger format and then fastqc ... the results are bad. Does anyone know the cause? I do not understand why. b) With the same sequences can know if they are different Rna and eliminate those that do not want to examine? merry christmas :)

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CEAS/Transcription Factor Binding sites
by Benjamin Osei-agyeman 16 Dec '13

16 Dec '13

Hi List, I am performing a chip seq experiment using CEAS in galaxy, i obtained the following output in pdf form: http://www.datafilehost.com/d/a9d75211 Could some one explain what the output from CEAS tells about the location of the binding sites for the dataset? Thanks in advance Benjy

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Estimated Fragment Lenghth/FDR
by Benjamin Osei-agyeman 16 Dec '13

16 Dec '13

Hi List, Could someone explain the Estimated Fragment length? How is it used in Peak detection? Again what files are used in calculating for the False Discovery Rate (FDR)? Thanks in advance Benjy

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Re: [galaxy-user] fastqc and blast?
by Jennifer Jackson 13 Dec '13

13 Dec '13

Hello Mark, Correct - not needed. Any Illumina data that results from a CASAVA 1.8 or higher pipeline is already has quality scores scaled to Sanger Phred with an ASCII offset of 33. This translates to the ".fastqsanger" format in Galaxy, so no grooming is required, you can just assign the datatype. How to do that is in the first link below. And all the details, including how to read a FastQC report to determine this is in the screencast. Thanks! Jen Galaxy team On 12/13/13 8:58 AM, Mark Lindsay wrote: > Hi James > > do you need to run the Groomer on the latest Illumina data? > > BW > > Mark > > > > On 13 Dec 2013, at 16:53, Jennifer Jackson <jen(a)bx.psu.edu > <mailto:jen@bx.psu.edu>> wrote: > >> Hello, >> >> For the first question, make sure that you are running the groomer >> with the correction options. In almost all cases for Illumina data >> this will mean leaving all but one setting at default. The setting to >> change is "Input FASTQ quality scores type:". The results of FastQC >> will inform you about how to set this. An example is in this wiki >> section's screencast plus the first bullet point: >> https://wiki.galaxyproject.org/Support#Dataset_special_cases >> http://vimeo.com/galaxyproject/fastqprep >> >> For the second, I am not sure what you mean by 'different'. Do you >> mean the data may have contamination from another species? Or that >> the the data content may be different with respect to quality? >> >> In short, to filter based on quality as reported in the FastQC >> report, try tools in the same tool group such as "FASTQ Trimmer" or >> "FASTQ Quality Trimmer". >> >> The protocols included in our RNA-seq pipeline help start out with >> some quality steps: >> https://wiki.galaxyproject.org/Support#Tools_on_the_Main_server:_RNA-seq >> >> And many from our community have contributed RNA-seq tutorials: >> https://wiki.galaxyproject.org/Learn#Other_Tutorials >> >> Hopefully this helps! >> >> Jen >> Galaxy team >> >> On 12/13/13 7:05 AM, Jorge Braun wrote: >>> Hello mates, >>> >>> I have two doubts galaxy: >>> >>> a) I have rna-seq data from Illumina and do fastqc ... the results >>> are good but when I fastgroomer to Sanger format and then fastqc ... >>> the results are bad. Does anyone know the cause? I do not understand >>> why. >>> >>> b) With the same sequences can know if they are different Rna and >>> eliminate those that do not want to examine? >>> >>> merry christmas :) >>> >>> >>> ___________________________________________________________ >>> The Galaxy User list should be used for the discussion of >>> Galaxy analysis and other features on the public server >>> atusegalaxy.org <http://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/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> >>> http://galaxyproject.org/search/mailinglists/ >> >> -- >> Jennifer Hillman-Jackson >> http://galaxyproject.org >> ___________________________________________________________ >> The Galaxy User list should be used for the discussion of >> Galaxy analysis and other features on the public server >> at usegalaxy.org <http://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/ >> >> To search Galaxy mailing lists use the unified search at: >> >> http://galaxyproject.org/search/mailinglists/ > -- Jennifer Hillman-Jackson http://galaxyproject.org

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Re: [galaxy-user] fastqc and blast?
by Jennifer Jackson 13 Dec '13

13 Dec '13

Hello Mark, Correct - no needed. Any Illumina data that results from a CASAVA 1.8 or higher pipeline is already has quality scores scaled to Sanger Phred with an ASCII offset of 33. This translates to the ".fastqsanger" format in Galaxy, so no grooming is required, you can just assign the datatype. How to do that is in the first link below. And all the details, including how to read a FastQC report to determine this is in the screencast. Thanks! Jen Galaxy team On 12/13/13 8:58 AM, Mark Lindsay wrote: > Hi James > > do you need to run the Groomer on the latest Illumina data? > > BW > > Mark > > > > On 13 Dec 2013, at 16:53, Jennifer Jackson <jen(a)bx.psu.edu > <mailto:jen@bx.psu.edu>> wrote: > >> Hello, >> >> For the first question, make sure that you are running the groomer >> with the correction options. In almost all cases for Illumina data >> this will mean leaving all but one setting at default. The setting to >> change is "Input FASTQ quality scores type:". The results of FastQC >> will inform you about how to set this. An example is in this wiki >> section's screencast plus the first bullet point: >> https://wiki.galaxyproject.org/Support#Dataset_special_cases >> http://vimeo.com/galaxyproject/fastqprep >> >> For the second, I am not sure what you mean by 'different'. Do you >> mean the data may have contamination from another species? Or that >> the the data content may be different with respect to quality? >> >> In short, to filter based on quality as reported in the FastQC >> report, try tools in the same tool group such as "FASTQ Trimmer" or >> "FASTQ Quality Trimmer". >> >> The protocols included in our RNA-seq pipeline help start out with >> some quality steps: >> https://wiki.galaxyproject.org/Support#Tools_on_the_Main_server:_RNA-seq >> >> And many from our community have contributed RNA-seq tutorials: >> https://wiki.galaxyproject.org/Learn#Other_Tutorials >> >> Hopefully this helps! >> >> Jen >> Galaxy team >> >> On 12/13/13 7:05 AM, Jorge Braun wrote: >>> Hello mates, >>> >>> I have two doubts galaxy: >>> >>> a) I have rna-seq data from Illumina and do fastqc ... the results >>> are good but when I fastgroomer to Sanger format and then fastqc ... >>> the results are bad. Does anyone know the cause? I do not understand >>> why. >>> >>> b) With the same sequences can know if they are different Rna and >>> eliminate those that do not want to examine? >>> >>> merry christmas :) >>> >>> >>> ___________________________________________________________ >>> The Galaxy User list should be used for the discussion of >>> Galaxy analysis and other features on the public server >>> atusegalaxy.org <http://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/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> >>> http://galaxyproject.org/search/mailinglists/ >> >> -- >> Jennifer Hillman-Jackson >> http://galaxyproject.org >> ___________________________________________________________ >> The Galaxy User list should be used for the discussion of >> Galaxy analysis and other features on the public server >> at usegalaxy.org <http://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/ >> >> To search Galaxy mailing lists use the unified search at: >> >> http://galaxyproject.org/search/mailinglists/ > -- Jennifer Hillman-Jackson http://galaxyproject.org

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Which tool to use for extract exon, codon information
by Tomaszewicz, Keith 11 Dec '13

11 Dec '13

Hi, I am new to galaxy but I think your tools may be what I need. I simply have a .bed file with amplicons and their chromosome, start and stop location in the human genome. I simply want to align the .bed file amplicons to the HG19 and have a file I can export that which will tell me what exons are covered by the amplicons. Is this possible? If so I have no idea how to do this yet using galaxy. Do I need to upload the HG19 or is that in your system already. Can codons that are covered by the start and stop locations be extracted as well.? Thanks keith ...................................................................... The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, transmission, re-transmission, dissemination or other use of, or taking of any action in reliance upon this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and delete the material from any computer.

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inconsistent BAM-to-SAM behavior
by Michael Mason 10 Dec '13

10 Dec '13

Hi, I have run some top hap output through the samtools BAM-to-SAM wrapper. It creates the SAM file about 50% of the time. The rest of the time it makes an empty file. In this case if I just rerun it often works. I was wondering if anyone else has seen this behavior. I am using a cloud server and think I might need to change some settings. This causes my workflow to fail for many libraries so I also interested in any workarounds anyone has figured out. Thanks in advance for any help. Cheers Mike ________________________________ --CONFIDENTIALITY NOTICE--: The information contained in this email is intended for the exclusive use of the addressee and may contain confidential information. If you are not the intended recipient, you are hereby notified that any form of dissemination of this communication is strictly prohibited. www.benaroyaresearch.org

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Workflow does not run
by garzetti 10 Dec '13

10 Dec '13

Hello! I have a question about a workflow I have created from my history. I can edit and view it, but when I try to run it, a white page appears and I cannot do anything. I have created other worflows which perfectly run, but I don't know why this one doesn't. It includes 4 steps for GATK pre-processing steps (Indel Realigner, Count Covariates and Table Recalibration). What can the problem be? I would appreciate any input! Thanks Debora

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My Galaxy runs are still not starting
by Afazja - mpm 10 Dec '13

10 Dec '13

Hi I have seen a similar posts on Galaxy mailing list and writing to you since my problems with Galaxy continues. I have jobs (Cofflinks and Tophat) which have been waiting to run for a more then 12 hours. Is there a problem with jobs running on Galaxy today? Many hanks Marcin

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How to filter the sequences containing not[ATCG] character？
by 朱师云 10 Dec '13

10 Dec '13

Hi Jen,As the title, I have a [fasta] file that obtained from a [gtf] file, >cuff102.1atcgtaaagggcgat>cuff103.1gtcgttgactNNNNNNNNgtc and I want to get the output like this to filter the sequences that contain any not[ATCG] character? >cuff102.1atcgtaaagggcgat I have a large of sequences to filter. I thought a way that firstly convert the file to [interval] file, and secondly SELECT the line not matching the patten /\t[ATCGatcg]*[^ATCGatcg]/.Am I right? Or there is a one-step way ?

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