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Fragment Recruitment Plot (version 1.0.0)
Dataset missing? See help below
Minimum identity to include in plot (y-axis extent)
Default to 0 for full length
(e.g. name of the reference genome). Default is the accession number of reference genome.
Optional subtitle
Color for plot points

What it does

This tool creates a fragment recruitment plot from a SAM input file. Its main purpose is to display a graph of aligned metagenomic reads against an organism's reference genome. The percent identity is calculated based on the MD: tag in the optional form field of the SAM format.


Input Datasets/Files

Two input types are required in this tool:

  1. Reference genome: the reference sequence in FASTA format used for alignment; it can be uploaded via Get Data -> Upload File.
  2. SAM format dataset: can be uploaded via Get Data -> Upload File. It can also be obtained after alignment with Bowtie2.

If using Bowtie2 output, follow these steps to format the file properly:

  1. Filter the BAM/SAM output from Bowtie2 by executing the "samtool_filter2" tool from the Tool Shed. More information can be found in this link: http://toolshed.g2.bx.psu.edu/view/devteam/samtool_filter2

  2. Use these options in the samtool_filter2:
    • Exclude Header
    • Minimum MAPQ quality score = 1

    TIP: This ensures the file contains all aligned reads without any missing MD tags per line.

  3. Convert BAM-to-SAM by using using the tool "bam_to_sam" installed from the Tool Shed. Additional information can be found in this link:: http://toolshed.g2.bx.psu.edu/view/devteam/bam_to_sam


Output Example

An example image (png format) of a fragment recruitment plot.

/repository/static/images/c6fdb2e063f8a90f/images%2Ffrp_output_small.png