Browse the page, use the Find command in your browser or use the Search box at the top right of the page to search the questions and answers. Galaxy Frequently Asked Questions 1. '''[#Galaxy What is Galaxy?]'''[[br]] [[br]] 1. '''[#localGalaxy How is our local Galaxy different from the main Galaxy?]'''[[br]] [[br]] 1. How can I '''[#upload upload big files into Galaxy?]'''[[br]] [[br]] 1. How much '''[#space space do I have in Galaxy?]'''[[br]] [[br]] 1. Is my data '''[#backed backed up?]'''[[br]] [[br]] 1. I have deleted data but Galaxy shows that I am still using the same number of Gb. '''[#dataDeletion Why?]'''[[br]] [[br]] 1. How do I '''[#findFastqFormat know if my fastq files are in Sanger or Solexa format?]'''[[br]] [[br]] 1. How do I '''[#convertFastqFile convert fastq files to fastqsanger format?]'''[[br]] [[br]] 1. How do I '''[#quality check the quality of my NGS reads?]'''[[br]] [[br]] 1. '''[#convertFastqFile2 I have uploaded a fastq file but it doesn't appear on the bowtie or tophat dropdown menus.]'''[[br]] [[br]] 1. How do I '''[#ChIP-seq analyze ChIP-seq data?]'''[[br]] [[br]] 1. How do I '''[#RNA-seq analyze RNA-seq data?]'''[[br]] [[br]] 1. How do I '''[#versions know the versions of the software that Galaxy is running?]'''[[br]] [[br]] 1. '''[#ceas1 The peak2gene for annotating ChIP-seq peaks doesn't work with my data]'''[[br]] [[br]] 1. How do I '''[#ceas2 annotate peaks for a genome that is not supported by the peak2gene tool?]'''[[br]] [[br]] 1. How do I '''[#bugReport report a bug or an error?]'''[[br]] [[br]] 1. How do I '''[#help2 get help with Galaxy]'''[[br]] [[br]] ---- Answers to Galaxy Frequently Asked Questions 1. [=#Galaxy What is Galaxy?] [[br]] [[br]] * Galaxy is a web based platform that makes many Unix bioinformatics tools available through a web interface. [[br]] [[br]] This is [https://main.g2.bx.psu.edu/ the main Galaxy site.][[br]] [[br]] This is [https://galaxy.wi.mit.edu/ the Whitehead Galaxy site.] '''Tools in this site are outdated now. We encourage users to contact BaRC to find alternative methods of analysis.''' [[br]] [[br]] 1. [=#localGalaxy How is our local Galaxy different from the main Galaxy?] [[br]] [[br]] * '''Our Galaxy site is not updated anymore and it is not backed up.''' [[br]] [[br]] * Data is stored and analyzed locally and it is not accessible outside Whitehead. The upload of big files is faster than if you had to send the files to the main Galaxy server.[[br]] [[br]] * Our local Galaxy contains many of the [https://main.g2.bx.psu.edu/ | main Galaxy] tools and most of the tools from the “NGS (next generation sequencing) Toolbox” for Illumina sequences. [[br]] Additionally, to have a more complete set of tools for analysis of NGS data we have added several tools from [http://cistrome.org/ap/ | Galaxy/Cistrome] and the [http://toolshed.g2.bx.psu.edu/ | Galaxy toolshed ]: * Removal of adaptors: Cutadapt. * Mapping: Bowtie2 and Tophat2 * Peak calling: MACs 1.4 * Peak annotation: Integrative Analysis tools and Bedtools * RNA-seq Analysis: Tophat2, Count tools and DE-seq.[[br]] [[br]] * Our local Galaxy contains several custom genomes: * ''S. cerevisiae'' coding ORFs * ''C. albicans'' (Ca21July2011) * Planarian superdupercontigs Oct 06 * Planarian BIMSB transcriptome * Planarian SMEDV2 transcriptome * ''Prochlorococcus marinus'' str.NATL2A (March2013)[[br]] [[br]] 1. [=#upload How can I '''upload big files into Galaxy?'''] [[br]] [[br]] * First you have to copy the files into your galaxy uploads folder, then you have to select the file and upload it through the Galaxy upload interface. * [http://iona.wi.mit.edu/bio/docs/GalaxyFAQs/UploadOfBigFilesInGalaxy.pdf | Click here for a more detailed description. ] [[br]] [[br]] 1. [=#space How much '''space do I have in Galaxy?'''] [[br]] [[br]] * 500 Gb[[br]] [[br]] 1. [=#backed '''Is my data backed up?'''] [[br]] [[br]] * No, data is not backed up in Galaxy. You should download your results to one of your lab drives.[[br]] [[br]] 1. [=#dataDeletion '''I have deleted data but Galaxy shows that I am still using the same number of Gb.'''] [[br]] [[br]] * You have to "''Purge Deleted Datasets''", on the history cog menu, to permanently remove data from the disk.[[br]] [[br]] 1. [=#findFastqFormat How do I '''know if my fastq files are in Sanger or Solexa format?'''] [[br]] [[br]] * You can run the "''FastQC''" tool, within the "''NGS: QC and manipulation''" tools, to find out the version of the quality encoding of your reads.[[br]] [[br]] 1. [=#convertFastqFile How do I '''convert fastq files to fastqsanger format?]''' [[br]] [[br]] * Use the "''FASTQ Groomer''" tool within the "''NGS: QC and manipulation''" tools. Make sure you select the correct "''Input FASTQ quality scores type''".[[br]] [[br]] 1. [=#quality How do I '''check the quality of my NGS reads?'''][[br]] [[br]] * Some options are the "''FastQC''" tool, and the "''Compute quality statistics''" plus "''Draw quality score boxplot''" tools within the "''NGS: QC and manipulation''" tools.[[br]] [[br]] 1. [=#convertFastqFile2 '''I have uploaded a fastq file but it doesn't appear on the bowtie or tophat dropdown menus.]'''[[br]] [[br]] * Only files in fastqsanger format will appear in the bowtie or tophat dropdown menus. You have to convert the fastq file to fastqsanger format using the "''FASTQ Groomer''" tool within the "''NGS: QC and manipulation''" tools.[[br]] [[br]] 1. [=#ChIP-seq How do I '''analyze ChIP-seq data?]'''[[br]] [[br]] * We have [http://iona.wi.mit.edu/bio/docs/GalaxyFAQs/ChIP-seq-AnalysisInGalaxy.pdf | detailed instructions for analysis of ChIP-seq data in Galaxy here.] [[br]] [[br]] 1. [=#RNA-seq How do I '''analyze RNA-seq data?]'''[[br]] [[br]] * We have [http://iona.wi.mit.edu/bio/docs/GalaxyFAQs/RNAseq-AnalysisInGalaxy.pdf | detailed instructions for analysis of RNA-seq data in Galaxy using the tuxedo tools here.] [[br]] [[br]] 1. [=#versions How do I '''know the versions of the that software Galaxy is running?]'''[[br]] [[br]] * These are the current versions of frequently used tools. * MACS: macs 1.4 * Bowtie: bowtie version 0.12.9 * Bowtie2: bowtie2-align version 2.1.0 * Tophat : TopHat v1.3.3 * Tophat2: TopHat v2.0.8 * Cufflinks: cufflinks v2.1.1 * Cuffcompare: cuffcompare v2.1.1 * Cuffmerge: merge_cuff_asms v1.0.0 * Cuffdiff: cuffdiff v2.1.1 * htseq-count: version 0.5.3p9[[br]] [[br]] * The version of many of the tools is specified on the command that was run. This information is found in the output dataset. [[br]] [[br]] 1. '''[=#ceas1 The ''peak2gene'' tool for annotating ChIP-seq peaks doesn't work with my data]'''[[br]] [[br]] * The [http://liulab.dfci.harvard.edu/CEAS/download.html |Cis-regulatory Element Annotation System] only provides background annotations for the following genomes: ce4 and ce6 for worm, dm2 and dm3 for fly, mm8 and mm9 for mouse, hg18 and hg19 for human. If the genome you are working with is not included on this list refer to next FAQ below.[[br]] [[br]] 1. [=#ceas2 How do I '''annotate peaks for a genome that is not supported by the ''peak2gene'' tool?]'''[[br]] [[br]] * See our [http://iona.wi.mit.edu/bio/docs/GalaxyFAQs/How_to_link_peaks_to_genes_in_Galaxy.pdf | Annotating peaks in Galaxy] page for detailed instructions.[[br]] [[br]] 1. [=#bugReport How do I '''report a bug or an error?]'''[[br]] [[br]] * If your job failed and resulted on a ''red'' dataset, you should click on the ''bug button'' within the Galaxy interface to report the error. * You can also report errors by creating a [https://nik.wi.mit.edu/trac/newticket | new ticket on the nik tracking system]. The system will request your email's username and password.[[br]] [[br]] 1. [=#help2 How do I '''get help with Galaxy?]'''[[br]] [[br]] * You can send Galaxy technical or scientific help requests creating a [https://nik.wi.mit.edu/trac/newticket | new ticket on the nik tracking system]. You will need your email's username and password.[[br]] [[br]]