galaxy-user April 2011

galaxy-user@lists.galaxyproject.org

86 participants
78 discussions

One question about the genome coordinates when using Fetch Sequences
by Sean 07 Apr '11

07 Apr '11

Hi, I have one stupid question. The coordinates of the region chr1 2351533 - 2351843 from UCSC (hg18) will retrieve 311 bases. However, when I use Fetch Sequences from galaxy, it will only retrieves 310 bases. Apparently, the first base of the 311 bases is missing from the Fetch Sequences result because the ending bases are the same. Does this mean that I need to modified the coordinates first and then use the Fetch Sequences to get the correct sequence? I thought UCSC and galaxy were both 0 base? Thanks. Sean

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Re: [galaxy-user] [galaxy-bugs] Cufflinks
by Jeremy Goecks 07 Apr '11

07 Apr '11

Hi Gabor, I'm moving your email to the galaxy-user mailing list because it concerns galaxy usage; also, there's a substantial community of users doing RNA-seq that may be able to offer suggestions to help you out. To your issue: > I used Galaxy (Bowtie) to successfully map 15 million Illumina reads trimmed to 65bp. When I applied Cufflinks to the BAM data no transcripts were reported even though it ran OK. It is possible that very little mapped to known exons in this data set. Does Cufflinks only report data for known transcripts? I thought it was designed to work without a reference annotation. How does it decide what qualifies as a transcript? Any ideas why I got such a result? Your problems are likely at least partially due to using Bowtie instead of Tophat. Tophat is the standard way to map reads so that Cufflinks can assemble transcripts. Cufflinks assembles transcript--de novo or reference-guided--based on the mapped reads, but mapped reads must include spliced reads, which are generated by Tophat but not Bowtie. Good luck, J.

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Regrading SNPs
by Nripesh Prasad 07 Apr '11

07 Apr '11

I wish to compare SNPs in my mouse sample (SNP file generated from Partek Genomic suite) with SNPs from UCSC browser. how do i do that on galaxy? Nripesh Prasad

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Re: [galaxy-user] Adding the Hydra genome to Galaxy
by Jennifer Jackson 07 Apr '11

07 Apr '11

Hello Rob, We will add this to our to-do list for new genomes. Thanks for sending the Genbank information! Next time, if you could send requests to galaxy-user, that would be very helpful for the team. Best, Jen Galaxy team On 1/3/11 12:37 PM, Rob Steele wrote: > Hi Jennifer, > Would it be possible to get the Hydra genome assembly added to Galaxy? > It has been published and is available in GenBank under accession number > ABRM00000000. > > Cheers, > Rob > > Rob Steele, Ph.D. > Professor > D240 Medical Sciences I > Department of Biological Chemistry > School of Medicine > University of California, Irvine > Irvine, CA 92697-1700 > > phone: 949-824-7341 > e-mail: resteele(a)uci.edu > fax: 949-824-2688 > web: http://polyp.biochem.uci.edu/wiki/index.php/Main_Page > -- Jennifer Jackson http://usegalaxy.org

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Re: [galaxy-user] galaxy-user Digest, Vol 58, Issue 3
by youngor Cheung 06 Apr '11

06 Apr '11

<< Graduate Student: Yanfeng Zhang Comparative Genomics Group. Kunming Institute of Zoology,Chinese Academy of Sciences. >> > From: galaxy-user-request(a)lists.bx.psu.edu > Subject: galaxy-user Digest, Vol 58, Issue 3 > To: galaxy-user(a)lists.bx.psu.edu > Date: Tue, 5 Apr 2011 11:33:23 -0400 > > 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: MAF (Eccles, David) > 2. Re: Analyzing Targeted Resequencing data with Galaxy > (Anton Nekrutenko) > 3. Re: MAF (Anton Nekrutenko) > 4. convert formats (Sher, Falak) > 5. Re: convert formats (Daniel Blankenberg) > 6. Subject: Analyzing Targeted Resequencing data with> Galaxy > (Jackie Lighten) > 7. Re: Analyzing Targeted Resequencing data with Galaxy > (Anton Nekrutenko) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 5 Apr 2011 14:33:35 +0200 > From: "Eccles, David" <david.eccles(a)mpi-muenster.mpg.de> > To: "Ross" <ross.lazarus(a)gmail.com> > Cc: galaxy-user(a)lists.bx.psu.edu > Subject: Re: [galaxy-user] MAF > Message-ID: > <B4B747BF2FE2BB43A6D483192168CBD172D0D5(a)VSM.exc.top.gwdg.de> > Content-Type: text/plain; charset="iso-8859-1" > > On Tue, Apr 5, 2011 at 5:19 AM, Laura Iacolina <liacolina(a)uniss.it> wrote: > > Considering I have to analyse 200 samples with 50K markers is there any way > to tell R to analyse each SNP one after the other? > > From: Ross [mailto:ross.lazarus@gmail.com] > > There are some Galaxy wrappers for plink > > (http://pngu.mgh.harvard.edu/~purcell/plink/) that may be useful for > > some kinds of analysis available in the rgenetics tools if you have > > linkage pedigree genotype and map files. > > I would also advise using plink for this. Calculating SNP marker statistics > [1] is the one of the things that it has been designed to do. The main > problem is getting data into a format supported by plink, either linkage (one > line per individual), or transposed pedigree (one line per marker). There are > details on these formats in the plink documentation [2]. > > [1] http://pngu.mgh.harvard.edu/~purcell/plink/summary.shtml#freq > [2] http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#tr > > -- > David Eccles (gringer) > > > > ------------------------------ > > Message: 2 > Date: Tue, 5 Apr 2011 09:56:44 -0400 > From: Anton Nekrutenko <anton(a)bx.psu.edu> > To: Lali <laurafe(a)gmail.com> > Cc: galaxy-user(a)lists.bx.psu.edu > Subject: Re: [galaxy-user] Analyzing Targeted Resequencing data with > Galaxy > Message-ID: <8172FBD2-4CDA-4312-B54F-DCC730A40AB9(a)bx.psu.edu> > Content-Type: text/plain; charset=us-ascii > > Lali: > > In your case the workflow for capture re-sequencing should look like this: > > 1. QC data (groom fastq files and plot quality distribution) > 2. Map the reads (use bwa) > 3. Generate and filter pileup > 4. Intersect pileup with coordinates of sure select bates. > > However, before you dive in please understand basic Galaxy functionality by taking a look at http://usegalaxy.org/galaxy101 and watching *all* Illumina-related Galaxy quickies (black boxes on the front page on Galaxy). Next, take a look at http://usegalaxy.org/heteroplasmy. > > Note, that we are working on bringing "industrial-strength" diploid genotyping functionality in Galaxy in the next two-three months that will include more sophisticated genotypers, recalibration and realignment tools, and novel visualization approaches. > > Thank for using Galaxy. > > anton > galaxy team > > > > On Apr 5, 2011, at 2:44 AM, Lali wrote: > > > Hi! > > I am having problems with my sequencing results, but I am a newbie at this; so I am thinking there is something wrong with my analysis. So far, I've tried Galaxy and CLC Workbench, but with CLC I could not align to the whole genome, only to individual chromosomes (maybe there is a way, but by the time the trial ended I had not found it). > > > > I used SureSelect capture kit and did single end sequencing on an Illumina. The files the lab sent me are FastQ Illumina 1.5 files, my samples were indexed, and I got a series of files each representing an Index. > > > > What would be the standard workflow for this kind of data? > > Which tools/settings? > > > > Does anyone have an example Galaxy workflow for preparing (clipping adapters, quality trimming) and mapping Targeted Resequencing Data? > > > > Is there a way to obtain a coverage report through Galaxy? > > > > Is it possible to ignore/discard the reads mapped when the coverage is below a certain threshold? > > > > I know, I know, a lot of things, but I am very lost. > > Any help is appreciated. > > > > L ___________________________________________________________ > > 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/ > > Anton Nekrutenko > http://nekrut.bx.psu.edu > http://usegalaxy.org > > > > > > > ------------------------------ > > Message: 3 > Date: Tue, 5 Apr 2011 10:09:44 -0400 > From: Anton Nekrutenko <anton(a)bx.psu.edu> > To: Laura Iacolina <liacolina(a)uniss.it> > Cc: galaxy-user(a)lists.bx.psu.edu > Subject: Re: [galaxy-user] MAF > Message-ID: <0E6E6AC6-0300-4B5E-B462-BA6715FC1F6A(a)bx.psu.edu> > Content-Type: text/plain; charset=windows-1252 > > Laura: > > SNP identification and analysis is a very complex subject and without knowing what you are trying to do it is very difficult to point you to the right direction. Perhaps a good place to start would be a supplement for the last year's report from 1000 Genomes Consortium (Nature. 467(7319): p. 1061-1073). Some of the steps you can perform through Galaxy, yet some are in development. > > Thanks! > > anton > galaxy team > > > On Apr 5, 2011, at 5:19 AM, Laura Iacolina wrote: > > > Dear all, > > I?m analysing SNPs data for the first time. I tried with the few software I found in litterature but they can only manage small datasets. I am currently trying with ?genetics? package in R but the Geno function takes into account a marker at a time. Considering I have to analyse 200 samples with 50K markers is there any way to tell R to analyse each SNP one after the other? > > > > Thank you very much for the help. > > > > Laura > > > > > > ___________________________________________________________ > > 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/ > > Anton Nekrutenko > http://nekrut.bx.psu.edu > http://usegalaxy.org > > > > > > > ------------------------------ > > Message: 4 > Date: Tue, 5 Apr 2011 10:21:38 -0400 > From: "Sher, Falak" <Falak.Sher(a)childrens.harvard.edu> > To: "galaxy-user(a)lists.bx.psu.edu" <galaxy-user(a)lists.bx.psu.edu> > Subject: [galaxy-user] convert formats > Message-ID: > <28032B153244774DA100823F4D4764210CBC2B2D6F(a)CHEXCCRV4.CHBOSTON.ORG> > Content-Type: text/plain; charset="iso-8859-1" > > Hi colleagues, > > I used MACS for peak finding through Galaxy, I want to convert the format of the resulted wig files into bigwig using Galaxy tool "convert formats' > The job is executed but not running, I redo even then it does not start. it is stucked with the message, job is waiting to run. > logout and re login are not helping > > any suggestion/information please ? > > F > > > > ------------------------------ > > Message: 5 > Date: Tue, 5 Apr 2011 10:30:47 -0400 > From: Daniel Blankenberg <dan(a)bx.psu.edu> > To: "Sher, Falak" <Falak.Sher(a)childrens.harvard.edu> > Cc: "galaxy-user(a)lists.bx.psu.edu" <galaxy-user(a)lists.bx.psu.edu> > Subject: Re: [galaxy-user] convert formats > Message-ID: <B7D82135-EF7A-4DD1-81F2-9A99C1BA2023(a)bx.psu.edu> > Content-Type: text/plain; charset=us-ascii > > Hi Falak, > > Due to the fact that the underlying wig to bigWig executable can use huge amounts of RAM, a single large-memory node is allocated for these jobs. This has the unfortunate side effect that wigToBigwig jobs may need to wait for a significant amount of time before being executed. Please be patient, although if you suspect a problem and have waited for a very long period of time, please do report it. > > Thanks for using Galaxy, > > Dan > > > On Apr 5, 2011, at 10:21 AM, Sher, Falak wrote: > > > Hi colleagues, > > > > I used MACS for peak finding through Galaxy, I want to convert the format of the resulted wig files into bigwig using Galaxy tool "convert formats' > > The job is executed but not running, I redo even then it does not start. it is stucked with the message, job is waiting to run. > > logout and re login are not helping > > > > any suggestion/information please ? > > > > F > > > > ___________________________________________________________ > > 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/ > > > > > ------------------------------ > > Message: 6 > Date: Tue, 05 Apr 2011 10:02:12 -0300 > From: Jackie Lighten <jc807177(a)dal.ca> > To: <galaxy-user(a)lists.bx.psu.edu> > Subject: [galaxy-user] Subject: Analyzing Targeted Resequencing data > with> Galaxy > Message-ID: <C9C09924.23C2%jc807177(a)dal.ca> > Content-Type: text/plain; charset="US-ASCII" > > You can do all the quality filtering with Galaxy, but may involve various > manipulations of the data. If I am not mistaken the "metagenomics" workflow > may help you out a little. Its designed for 454 data but should give you an > idea of how to go about things. There is a video tutorial on the site for > this workflow. > > A good place for you to start, however, may be here: Subject: > http://edwards.sdsu.edu/prinseq_beta/# > > Prinseq is easy to use and will give you a full break down of your raw data > and enables you to filter by quality/length etc. > > FASTqc is an Illumina specialized preliminary analysis tool: > http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/ > > I my self was not very impressed with CLC at all. It lacks very rudimentary > yet critical functions. > > I am currently working on population amplicon data so couldn't really help > you too much in the latest mapping to reference advances, but I found the > Lasergene SEQman mapping and de-nova assembler much better than the CLC > assembler. > Good luck > > Jack > > On 11 > > > > Message: 6 > > Date: Tue, 5 Apr 2011 08:44:06 +0200 > > From: Lali <laurafe(a)gmail.com> > > To: galaxy-user(a)lists.bx.psu.edu > > Subject: [galaxy-user] Analyzing Targeted Resequencing data with > > Galaxy > > Message-ID: <BANLkTin1ShWLQQ46+mFFBcxS-dO1GJuw_A(a)mail.gmail.com> > > Content-Type: text/plain; charset="iso-8859-1" > > > > Hi! > > I am having problems with my sequencing results, but I am a newbie at this; > > so I am thinking there is something wrong with my analysis. So far, I've > > tried Galaxy and CLC Workbench, but with CLC I could not align to the whole > > genome, only to individual chromosomes (maybe there is a way, but by the > > time the trial ended I had not found it). > > > > I used SureSelect capture kit and did single end sequencing on an Illumina. > > The files the lab sent me are FastQ Illumina 1.5 files, my samples were > > indexed, and I got a series of files each representing an Index. > > > > What would be the standard workflow for this kind of data? > > Which tools/settings? > > > > Does anyone have an example Galaxy workflow for preparing (clipping > > adapters, quality trimming) and mapping Targeted Resequencing Data? > > > > Is there a way to obtain a coverage report through Galaxy? > > > > Is it possible to ignore/discard the reads mapped when the coverage is below > > a certain threshold? > > > > I know, I know, a lot of things, but I am very lost. > > Any help is appreciated. > > > > L > > > > > > > ------------------------------ > > Message: 7 > Date: Tue, 5 Apr 2011 11:33:18 -0400 > From: Anton Nekrutenko <anton(a)bx.psu.edu> > To: Lali <laurafe(a)gmail.com> > Cc: galaxy-user <galaxy-user(a)lists.bx.psu.edu> > Subject: Re: [galaxy-user] Analyzing Targeted Resequencing data with > Galaxy > Message-ID: <C33F2B26-C075-47FC-B2F7-9D468ED3ED0E(a)bx.psu.edu> > Content-Type: text/plain; charset="us-ascii" > > Lali: > > Please, always CC mailing list when you reply. > > > My only problem with Galaxy is that I have to keep on clearing my cache in order to get the history to display correctly, is there another way of solving this issue? > > > Which browser/OS are your using? > > Thanks, > > anton > galaxy team > > On Apr 5, 2011, at 11:25 AM, Lali wrote: > > > Thanks so much for the tips Anton! > > I am very excited about the newer developments. > > I did watch the quickies and they were very useful for a beginner like me, I actually did my first try at the alignment by following the Illumina single-end tutorial video step by step, but you need to watch the paired-end too, for some of the first steps, which are explained better on that one. > > I have been playing around a lot with Galaxy, and I have several workflows, my department just started doing sequencing, so we don't have standard procedures set in place. I was assigned to evaluate Galaxy and CLC, and so far CLC has not impressed me, except for the fact that it can generate reports easily. > > I think Galaxy is the way to go for me (us, if I can convince them to run a local server), since I am not a bioinformatician, and just the fact that you can queue up actions and just walk away is fantastic (amongst other things). > > But because I am a beginner, I am not 100% of the settings I have chosen and my data is not looking too good so far, but I am having a bioinformatician come over and help me on Thursday and I think your tips will be of help. > > My only problem with Galaxy is that I have to keep on clearing my cache in order to get the history to display correctly, is there another way of solving this issue? > > > > Best regards, > > > > L > > > > On Tue, Apr 5, 2011 at 3:56 PM, Anton Nekrutenko <anton(a)bx.psu.edu> wrote: > > Lali: > > > > In your case the workflow for capture re-sequencing should look like this: > > > > 1. QC data (groom fastq files and plot quality distribution) > > 2. Map the reads (use bwa) > > 3. Generate and filter pileup > > 4. Intersect pileup with coordinates of sure select bates. > > > > However, before you dive in please understand basic Galaxy functionality by taking a look at http://usegalaxy.org/galaxy101 and watching *all* Illumina-related Galaxy quickies (black boxes on the front page on Galaxy). Next, take a look at http://usegalaxy.org/heteroplasmy. > > > > Note, that we are working on bringing "industrial-strength" diploid genotyping functionality in Galaxy in the next two-three months that will include more sophisticated genotypers, recalibration and realignment tools, and novel visualization approaches. > > > > Thank for using Galaxy. > > > > anton > > galaxy team > > > > > > > > On Apr 5, 2011, at 2:44 AM, Lali wrote: > > > > > Hi! > > > I am having problems with my sequencing results, but I am a newbie at this; so I am thinking there is something wrong with my analysis. So far, I've tried Galaxy and CLC Workbench, but with CLC I could not align to the whole genome, only to individual chromosomes (maybe there is a way, but by the time the trial ended I had not found it). > > > > > > I used SureSelect capture kit and did single end sequencing on an Illumina. The files the lab sent me are FastQ Illumina 1.5 files, my samples were indexed, and I got a series of files each representing an Index. > > > > > > What would be the standard workflow for this kind of data? > > > Which tools/settings? > > > > > > Does anyone have an example Galaxy workflow for preparing (clipping adapters, quality trimming) and mapping Targeted Resequencing Data? > > > > > > Is there a way to obtain a coverage report through Galaxy? > > > > > > Is it possible to ignore/discard the reads mapped when the coverage is below a certain threshold? > > > > > > I know, I know, a lot of things, but I am very lost. > > > Any help is appreciated. > > > > > > L ___________________________________________________________ > > > 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/ > > > > Anton Nekrutenko > > http://nekrut.bx.psu.edu > > http://usegalaxy.org > > > > > > > > > > Anton Nekrutenko > http://nekrut.bx.psu.edu > http://usegalaxy.org > > > >

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Re: [galaxy-user] [Genome] UCSC browser, access from Galaxy
by Hiram Clawson 05 Apr '11

05 Apr '11

Good Morning Dr. Hunt: Can you please clarify what upload function from galaxy you are trying to perform ? Perhaps the galaxy user help email list could direct you to advice on this subject ? (copied on this email) The Ensembl genome browser accepts the same types of upload tracks as does the UCSC genome browser. --Hiram ----- Original Message ----- From: "Pustulka-Hunt Elzbieta (SystemsX.ch)" <ela.hunt(a)systemsx.ch> To: genome(a)soe.ucsc.edu Sent: Thursday, March 31, 2011 5:19:55 AM Subject: [Genome] USCS browser, access from Galaxy Connection refused Couldn't connect to 127.0.0.1 8080 Couldn't open http://127.0.0.1:8080/root/display_as?id=27&display_app=ucsc&authz_method=d… Hi, I have a local installation of Galaxy. Is it at all possible to upload (easily) data from Galaxy to your browser? I have no trouble uploading an extra track to Ensembl. Could you support such access? Regards Ela ------------------------------------------------------------------------------------------------ Dr Ela Hunt SyBIT Deputy Project Manager Clausiusstr. 45, CLP D 2 ETHZ, CH-8092 Zurich +41 44 632 93 37 https://wiki.systemsx.ch/display/~ela.hunt@systemsx.ch/Dr+Ela+Hunt

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Recall: Upload file size and user authorization
by Paul-Michael Agapow 05 Apr '11

05 Apr '11

Paul-Michael Agapow would like to recall the message, "[galaxy-user] Upload file size and user authorization". ----------------------------------------- ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk **************************************************************************

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storage space/processor speed
by Keith E. Giles 05 Apr '11

05 Apr '11

I am trying to perform a "join" on two sets of intervals. There are ~20,000 intervals in one dataset and about 13 million on the other. This has been running for about 3 days now, and I'm pretty certain that its not going to work. Is there a way to know if there is enough memory available for a given function to run ahead of time? Also, how much storage space does each account have available? I know that one can access cloud space online, through amazon for example. However that seems to be fairly complicated and a bit out of reach for me for the short term.

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error on indel analysis
by Evan Schwab 05 Apr '11

05 Apr '11

Hi, I am receiving the following error when I try to run the Indel Analysis tool on a sam file. I kept the Frequency threshold at the default 0.015. Traceback (most recent call last): File "/galaxy/home/g2main/galaxy_main/tools/indels/indel_analysis.py", line 227, in if __name__=="__main__": __main__() File "/galaxy/home/g2main/galaxy_main/tools/indels/indel_analysis.py", line 84, in __main__ add_to_mis_matches( mis_matches[ chrom ], pos, bases ) File "/galaxy/home/g2main/galaxy_main/tools/indels/indel_analysis.py", line 34, in add_to_mis_matches mis_matches[ pos + j ] = { base: 1 } MemoryError Prior to that I tried with Frequency threshold 0.0 and it ran for days on end without any results. And I've tried Frequency threshold of 0.10 and it gave and error that said "Killed" with no explaination. Is there an error with the tool? Thanks Evan -- Evan Schwab Research Associate Megason Lab Department of Systems Biology Harvard Medical School 200 Longwood Ave Boston, MA 02115 908-938-3779

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convert formats
by Sher, Falak 05 Apr '11

05 Apr '11

Hi colleagues, I used MACS for peak finding through Galaxy, I want to convert the format of the resulted wig files into bigwig using Galaxy tool "convert formats' The job is executed but not running, I redo even then it does not start. it is stucked with the message, job is waiting to run. logout and re login are not helping any suggestion/information please ? F

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galaxy-user April 2011