short_reads_figure_score.py $input1 $output1 rpy

.. class:: warningmark To use this tool, your dataset needs to be in the *Quality Score* format. Click the pencil icon next to your dataset to set the datatype to *Quality Score* (see below for examples). ----- **What it does** This tool takes Quality Files generated by Roche (454), Illumina (Solexa), or ABI SOLiD machines and builds a graph showing score distribution like the one below. Such graph allows you to perform initial evaluation of data quality in a single pass. ----- **Examples of Quality Data** Roche (454) or ABI SOLiD data:: >seq1 23 33 34 25 28 28 28 32 23 34 27 4 28 28 31 21 28 Illumina (Solexa) data:: -40 -40 40 -40 -40 -40 -40 40 ----- **Output example** Quality scores are summarized as boxplot (Roche 454 FLX data): .. image:: ../static/images/short_reads_boxplot.png where the **X-axis** is coordinate along the read and the **Y-axis** is quality score adjusted to comply with the Phred score metric. Units on the X-axis depend on whether your data comes from Roche (454) or Illumina (Solexa) and ABI SOLiD machines: - For Roche (454) X-axis (shown above) indicates **relative** position (in %) within reads as this technology produces reads of different lengths; - For Illumina (Solexa) and ABI SOLiD X-axis shows **absolute** position in nucleotides within reads. Every box on the plot shows the following values:: o <---- Outliers o -+- <---- Upper Extreme Value that is no more | than box length away from the box | +--+--+ <---- Upper Quartile | | +-----+ <---- Median | | +--+--+ <---- Lower Quartile | | -+- <---- Lower Extreme Value that is no more than box length away from the box o <---- Outlier