wiki:GalaxyFAQs

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Galaxy Frequently Asked Questions

  1. What is Galaxy?

  2. How is our local Galaxy different from the main Galaxy?

  3. How can I upload big files into Galaxy?

  4. How much space do I have in Galaxy?

  5. Is my data backed up?

  6. I have deleted data but Galaxy shows that I am still using the same number of Gb. Why?

  7. How do I know if my fastq files are in Sanger or Solexa format?

  8. How do I convert fastq files to fastqsanger format?

  9. How do I check the quality of my NGS reads?

  10. I have uploaded a fastq file but it doesn't appear on the bowtie or tophat dropdown menus.

  11. How do I analyze ChIP-seq data?

  12. How do I analyze RNA-seq data?

  13. How do I know the versions of the software that Galaxy is running?

  14. The peak2gene for annotating ChIP-seq peaks doesn't work with my data

  15. How do I annotate peaks for a genome that is not supported by the peak2gene tool?

  16. How do I report a bug or an error?

  17. How do I get help with Galaxy

Answers to Galaxy Frequently Asked Questions

  1. What is Galaxy?

    • Galaxy is a web based platform that makes many Unix bioinformatics tools available through a web interface.

      This is ​the main Galaxy site.

      This is ​the Whitehead Galaxy site. Tools in this site are outdated now. We encourage users to contact BaRC to find alternative methods of analysis.

  2. How is our local Galaxy different from the main Galaxy?

    • Our Galaxy site is not updated anymore and it is not backed up.

    • 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.

    • Our local Galaxy contains many of the ​| main Galaxy tools and most of the tools from the “NGS (next generation sequencing) Toolbox” for Illumina sequences.
      Additionally, to have a more complete set of tools for analysis of NGS data we have added several tools from ​| Galaxy/Cistrome and the ​| 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.

    • 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)

  3. How can I upload big files into Galaxy?

  4. How much space do I have in Galaxy?

    • 500 Gb

  5. Is my data backed up?

    • No, data is not backed up in Galaxy. You should download your results to one of your lab drives.

  6. I have deleted data but Galaxy shows that I am still using the same number of Gb.

    • You have to "Purge Deleted Datasets", on the history cog menu, to permanently remove data from the disk.

  7. How do I know if my fastq files are in Sanger or Solexa format?

    • 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.

  8. How do I convert fastq files to fastqsanger format?

    • Use the "FASTQ Groomer" tool within the "NGS: QC and manipulation" tools. Make sure you select the correct "Input FASTQ quality scores type".

  9. How do I check the quality of my NGS reads?

    • Some options are the "FastQC" tool, and the "Compute quality statistics" plus "Draw quality score boxplot" tools within the "NGS: QC and manipulation" tools.

  10. I have uploaded a fastq file but it doesn't appear on the bowtie or tophat dropdown menus.

    • 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.

  11. How do I analyze ChIP-seq data?

  12. How do I analyze RNA-seq data?

  13. How do I know the versions of the that software Galaxy is running?

    • 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

    • The version of many of the tools is specified on the command that was run. This information is found in the output dataset.

  14. The peak2gene tool for annotating ChIP-seq peaks doesn't work with my data

    • The ​|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.

  15. How do I annotate peaks for a genome that is not supported by the peak2gene tool?

  16. How do I report a bug or an error?

    • 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 ​| new ticket on the nik tracking system. The system will request your email's username and password.

  17. How do I get help with Galaxy?

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