Re: [galaxy-user] Gene BED to codon BED not working properly
Hi Anthony, There are no known problems with the gene/codon BED tool, but if you have an example of a problem, I will take a look. Some items to double check first: 1 - Input is a BED 12 file 2 - Keep in mind that coordinates are "0-based, half-open start, fully closed end" and always reported with respect to the forward strand. Notation for bases 1-100 of a sequence would be written as: [0,100) More details are at: http://wiki.g2.bx.psu.edu/Learn/Datatypes#Bed 3 - This can make the math a bit tricky for transcripts aligning to the negative strand. This wiki by Angie at UCSC is definitely the best at explaining how to manipulate this type of data: http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms If you still think there is an issue, create a simple test of just a single or few transcripts with the problems in a dataset, run the tool, then tell me what you think is exactly wrong. Share the history using "Options" (gear icon) -> Share or publish -> generate a share link, copy, and send that back along with your comments to to my email address directly (only). Simple is best, so that we can narrow down the exact issue. For the aaChanges, this tool will work with most native Galaxy reference genomes (the tool group name is confusing, sorry!). Just set the build to be the same for all inputs. Stick with full builds (not variants - e.g. use mm9, not mm9female). If you get an error about a missing build, write back and I can let you know if the build is native or not, or possibly even add it to the index if it was previously excluded for some reason that no longer applies. Custom reference genomes are not available for this tool, so if it does turn out that the public Galaxy instance cannot make your particular build available, a local install would be the alternative: http://getgalaxy.org If you work out the gene/codon BED coordinates based on the additional info, please reply to the list to let us know. If not, I'll just watch for your shared link, Best, Jen Galaxy team On 7/11/12 2:07 PM, Antony Jose wrote: Hi, When using the gene BED to codon BED tool, I noticed that it is not accurately reporting the codons that make up a gene. For example, some of the codon are missing (particularly ones that span exon-exon junctions. Also, when changing reading frame from one exon to the next, the codons are not read appropriately and the reading frame appears to be decided arbitrarily. Is this a serious known flaw with the tool or am I missing something? Also, is there a version of aaChanges tool that can be used with any genome (not just human genome?). Thank you. Antony ___ 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/ -- Jennifer 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. 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/
[galaxy-user] Gene BED to codon BED not working properly
Hi, When using the gene BED to codon BED tool, I noticed that it is not accurately reporting the codons that make up a gene. For example, some of the codon are missing (particularly ones that span exon-exon junctions. Also, when changing reading frame from one exon to the next, the codons are not read appropriately and the reading frame appears to be decided arbitrarily. Is this a serious known flaw with the tool or am I missing something? Also, is there a version of aaChanges tool that can be used with any genome (not just human genome?). Thank you. Antony ___ 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/
Re: [galaxy-user] Initial QC and grooming for Illumina HiSeq2000 paired end RNAseq data
Hello Lindsey, Would you please send in a bug report from the FastQC error dataset that resulted from the run where you included running the Groomer tool first? This will help us to track down the problem. Please be sure to leave all datasets in your history for this run undeleted and in the original history that they were executed in. If you need to undelete, use "Option (gear icon) -> View Deleted Datasets", the click on the links to undelete. We will need the original inputs and full path through tools run in Galaxy. http://wiki.g2.bx.psu.edu/Support#Reporting_tool_errors Please include this email address in the bug report notes if your Galaxy account uses a different one. Thanks and I will watch for your bug report, Jen Galaxy team On 7/11/12 5:32 AM, Lindsey Kelly wrote: Good Morning, I confirmed with Illumina that my reads are in Sanger FASTQ format and used edit attributes to change them to fastqsanger. Then I joined the forward and reverse and ran the FastQ Joiner and the FastQC on the joined data file. I'm getting the following error: ## odpath=None: No output found in None. Output for the run was: Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/space/g2main Started analysis of FASTQ Analysis complete for FASTQ Failed to process file FASTQ java.lang.IllegalArgumentException: No known encodings with chars < 33 (Yours was ) at uk.ac.bbsrc.babraham.FastQC.Sequence.QualityEncoding.PhredEncoding.getFastQEncodingOffset(PhredEncoding.java:33) at uk.ac.bbsrc.babraham.FastQC.Modules.PerBaseQualityScores.getPercentages(PerBaseQualityScores.java:70) at uk.ac.bbsrc.babraham.FastQC.Modules.PerBaseQualityScores.raisesError(PerBaseQualityScores.java:164) at uk.ac.bbsrc.babraham.FastQC.Report.HTMLReportArchive.startDocument(HTMLReportArchive.java:194) at uk.ac.bbsrc.babraham.FastQC.Report.HTMLReportArchive.(HTMLReportArchive.java:59) at uk.ac.bbsrc.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:157) at uk.ac.bbsrc.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:108) at java.lang.Thread.run(Thread.java:662) I thought that perhaps this was because I just changed the file format and maybe they really aren't in Fastqsanger format, so I: changed the format back to fastq, ran the groomer, joined them and then ran the FastQC and received the same error. I also tried to join them first and then run the groomer, but the files don't show up if I haven't changed the attributes to Fastqsanger (which makes sense if Galaxy only uses fastqsanger files). I'm not sure what to try next. Thank you Lindsey On Wed, Jul 4, 2012 at 3:53 PM, Jennifer Jackson mailto:j...@bx.psu.edu>> wrote: Hello Lindsey, Yes, you have this correct. The general path would be to: - join forward and reverse data per run - run FASTQ Groomer & FastQC (note: if your data is already in Sanger FASTQ format with Phred+33 quality scaled values, the datatype '.fastqsanger' can be directly assigned and the FASTQ Groomer step skipped. This is likely true if your data is a from the latest CASAVA pipeline, but please double check.) - discard data as needed based on quality - split forward and reverse data that passes QC - concatenate all forward reads from a sample into one FASTQ file - concatenate all reverse reads from a sample into one FASTQ file. - for each sample, run TopHat using the two concatenated FASTQ files To manipulate paired end data, please see the tools -> NGS: QC and manipulation: FASTQ splitter & FASTQ joiner. To combined data files head-to-tail from multiple runs into a single FASTQ file please see the tool -> Text Manipulation: Concatenate datasets. I am not sure of the actual volume of data, but if these start to get large or TopHat errors with a memory problem, a local or cluster instance would be the recommendation: http://getgalaxy.org For reference: http://tophat.cbcb.umd.edu/manual.html http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html Hopefully this helps. Others are welcome to post comments/suggestions. Jen Galaxy team On 7/2/12 11:17 AM, Lindsey Kelly wrote: I am trying to do RNAseq analysis on Paired end data from the Hiseq2000. I have about 50 files for each sample (25 forward and 25 reverse - although each sample has a different number of files). I think that I need to: -convert them into FASTQ sanger format using the FASTSQ groomer tool -check the quality using the FASTQqc tool I don't know how to handle this many files. Do I have to groom and run the QC for each file? Should I join the paired files and run both tools on each pair, or should I combine all of the data for each sample (which I don't know how to do) and then groom and run the QC for all of the reads fo
Re: [galaxy-user] Initial QC and grooming for Illumina HiSeq2000 paired end RNAseq data
Good Morning, I confirmed with Illumina that my reads are in Sanger FASTQ format and used edit attributes to change them to fastqsanger. Then I joined the forward and reverse and ran the FastQ Joiner and the FastQC on the joined data file. I'm getting the following error: ## odpath=None: No output found in None. Output for the run was: Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/space/g2main Started analysis of FASTQ Analysis complete for FASTQ Failed to process file FASTQ java.lang.IllegalArgumentException: No known encodings with chars < 33 (Yours was ) at uk.ac.bbsrc.babraham.FastQC.Sequence.QualityEncoding.PhredEncoding.getFastQEncodingOffset(PhredEncoding.java:33) at uk.ac.bbsrc.babraham.FastQC.Modules.PerBaseQualityScores.getPercentages(PerBaseQualityScores.java:70) at uk.ac.bbsrc.babraham.FastQC.Modules.PerBaseQualityScores.raisesError(PerBaseQualityScores.java:164) at uk.ac.bbsrc.babraham.FastQC.Report.HTMLReportArchive.startDocument(HTMLReportArchive.java:194) at uk.ac.bbsrc.babraham.FastQC.Report.HTMLReportArchive.(HTMLReportArchive.java:59) at uk.ac.bbsrc.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:157) at uk.ac.bbsrc.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:108) at java.lang.Thread.run(Thread.java:662) I thought that perhaps this was because I just changed the file format and maybe they really aren't in Fastqsanger format, so I: changed the format back to fastq, ran the groomer, joined them and then ran the FastQC and received the same error. I also tried to join them first and then run the groomer, but the files don't show up if I haven't changed the attributes to Fastqsanger (which makes sense if Galaxy only uses fastqsanger files). I'm not sure what to try next. Thank you Lindsey On Wed, Jul 4, 2012 at 3:53 PM, Jennifer Jackson wrote: > Hello Lindsey, > > Yes, you have this correct. The general path would be to: > > - join forward and reverse data per run > - run FASTQ Groomer & FastQC >(note: if your data is already in Sanger FASTQ format with Phred+33 > quality scaled >values, the datatype '.fastqsanger' can be directly assigned and the > FASTQ Groomer > step skipped. This is likely true if your data is a from the latest > CASAVA pipeline, but >please double check.) > - discard data as needed based on quality > - split forward and reverse data that passes QC > - concatenate all forward reads from a sample into one FASTQ file > - concatenate all reverse reads from a sample into one FASTQ file. > - for each sample, run TopHat using the two concatenated FASTQ files > > To manipulate paired end data, please see the tools -> NGS: QC and > manipulation: FASTQ splitter & FASTQ joiner. > > To combined data files head-to-tail from multiple runs into a single FASTQ > file please see the tool -> Text Manipulation: Concatenate datasets. > > I am not sure of the actual volume of data, but if these start to get > large or TopHat errors with a memory problem, a local or cluster instance > would be the recommendation: http://getgalaxy.org > > For reference: > http://tophat.cbcb.umd.edu/manual.html > http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html > > Hopefully this helps. Others are welcome to post comments/suggestions. > > Jen > Galaxy team > > > On 7/2/12 11:17 AM, Lindsey Kelly wrote: > > I am trying to do RNAseq analysis on Paired end data from the Hiseq2000. > I have about 50 files for each sample (25 forward and 25 reverse - although > each sample has a different number of files). > > I think that I need to: > > -convert them into FASTQ sanger format using the FASTSQ groomer tool > > -check the quality using the FASTQqc tool > > > > I don't know how to handle this many files. Do I have to groom and run > the QC for each file? Should I join the paired files and run both tools on > each pair, or should I combine all of the data for each sample (which I > don't know how to do) and then groom and run the QC for all of the reads > for the sample. > > > Thanks in advance for advice > > Lindsey > > > ___ > 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/ > > > -- > Jennifer Jacksonhttp://galaxyproject.org > > > > -- Lindsey M Kelly University of Pittsburgh Cellular and Molecular Pathology Program Yuri Nikiforov Laboratory 412-578-9208 ___ The Galaxy User list should
[galaxy-user] metagenomics question
Hello, The publication and supplemental material for the metagenomics data and tools available in Galaxy described in: Windshield splatter analysis with the Galaxy metagenomic pipeline is available on the main public Galaxy instance at: Shared Data -> Shared Published Pages -> Windshield Splatter http://genome.cshlp.org/content/19/11/2144 http://main.g2.bx.psu.edu/u/aun1/p/windshield-splatter All methods and tools are explained in detail, including example datasets, histories, workflows, and scientific discussion of results. Hopefully this help. Going forward, please send new questions as a brand new thread (not as a reply to an older thread) directly to our mailing list at galaxy-u...@bx.psu.edu. http://wiki.g2.bx.psu.edu/Support#Public_mailing_list_Q_.26_A_discussions Best, Jen Galaxy team On 7/7/12 1:33 AM, Swayamprakash Patel wrote:> Hello, >i had run galaxy server for metagenomics study... but, i would like > to know that which database is used for the comparison... because in my > sample it had gives me highest no. of eukaryotic community. but actually > in my data there would be a bacterial community is present in more > numbers. that's why i have a question like this. -- Jennifer 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. 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/
