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What to do if I have a problem?

Please check if your issue has been reported on our RiboGalaxy Forum. If not, post your query on the forum and we will try to address it as soon as we can.


Alignments to a transcriptome

For alignments to a transcriptome, you will need to upload a reference transcriptome FASTA file. One option to get a transcriptome FASTA file is to use the UCSC Main table browser under "Get Data" on LHS and output the data in sequence format. Below we describe the procedure for obtaining the RefSeq Human transcriptome:

  • Select "Human" genome under the "Mammal" clade
  • Select "Gene and Gene Predictions" under Group and "RefSeq Genes" under Track
  • Select "refGene" under Table
  • Select "genome" for the Region
  • Select "sequence" as the output format
  • Send output to Galaxy
  • Click on the "get output" button
  • Select "mRNA" in the "Select sequence type for RefSeq Genes" page and submit


Alignments to a genome

For alignments to a genome, the easiest option is to use the published workflows for the genomes that are currently available in GWIPS-viz, by following the instructions below.

You can modify the parameters of the workflows. Alternatively you may want to have more control by using the tools individually. In this case, see the section on using the tools under "GWIPS-viz Mapping".

If your genome is not listed in the Published Workflows, see the section "If your genome is not in GWIPS-viz".

Workflow instructions for genomes in GWIPS-viz




RiboGalaxy workflow outputs

The following file types are the outputs from the RiboGalaxy workflows. However, only the BAM file and the two bigWig files are displayed in your history by default.

  • Cutadapt report - summary of the adaptor clipping.
  • Trimmed FASTQ file - output from Cutadapt.
  • SAM file of alignments to rRNA - output of reads mapped to the rRNA sequences using bowtie.
  • FASTQ file of unmapped reads - reads that were not mapped to the rRNA sequences using bowtie.
  • SAM file of alignments to the genome - output of reads mapped to the genome using bowtie.
  • BAM file of alignments to the genome - bowtie SAM output converted to BAM format.
  • BigWig file of ribo-seq coverage plots - BAM output converted to bigWig format for display in GWIPS-viz
  • BigWig file of ribosome profiles - ribosome profiles generated for display in GWIPS-viz


If you need to access any of the intermediary output files, you can unhide them in your history.

We recommend that you download the output files as they will be stored for a short time only on our server. In particular we recommend that you download the BAM alignment file (or SAM file if preferred) by clicking on the "Download" button when you click on the file in your History. You can also download the bigWig files which can be uploaded at any time to GWIPS-viz as Custom Tracks.



Using the tools under "GWIPS-viz Mapping"?

Instead of using the GWIPS-viz pipeline workflows, you may prefer to use the individual tools in the "GWIPS-viz Mapping" suite.


The recommended pipeline order is:

  1. Run Cutadapt to remove the adaptor linker sequence.

  2. Remove ribosomal RNA (rRNA) using Bowtie. The reads not mapped to the rRNA can then be aligned to the genome of interest.

  3. Align to the genome using Bowtie. This will produce a SAM file of the alignments. However the SAM format can be very big. Hence we recommend converting the SAM file to BAM format using the SAM-to-BAM tool in the "Convert Formats" suite.

  4. If you wish to view your alignments as a custom track in GWIPS-viz, you can generate ribo-seq coverage plots or ribosome profiles.

  • Ribo-seq coverage plots display the number of reads that cover a given genomic coordinate. You need to convert the BAM file to bigWig format using the "BAM to BigWig" tool in the Convert Formats suite. Providing the genome is in GWIPS-viz, a link will appear for display in GWIPS-viz. If the genome is not in GWIPS-viz, you can visualize the alignments in Trackster (see the section on "Genome not in GWIPS-viz").


  • For the eukaryotic data sets, ribosome profiles display the number of footprint reads at a particular genomic coordinate that align to the A-site (elongating ribosomes) or P-site (initiating ribosomes) of the ribosome, depending on the antibiotic used in the study. To generate a ribosome profile, select the "Generate ribosome profile from bowtie output (RNase 1 data)". The input file should be in BAM format. Enter the name for the ribosome profile track and enter the value for the offset to correspond to the ribosome decoding center. The offset is set to 15 by default. However, do modify the offset value to correspond to your own data.


  • For the prokaryotic data sets, a weighted centred approach (Oh et al., 2011) is used to indicate the positions of ribosomes. Select the "Generate ribosome profile from bowtie output (MNase data)". The input file should be in BAM format. Enter the name for the ribosome profile track and execute.


If your genome is not in GWIPS-viz

If the genome is not in GWIPS-viz, you can still pre-process and align your raw data using the tools in the GWIPS-viz suite. While you will not be able to visualize the alignments in GWIPS-viz, you can still visualize them using the Galaxy Trackster in RiboGalaxy.

Here's an outline of what you need to do: