Canonical Distribution Tool

Just finished creating a new tool for quality control. It is available starting in EP version 1.6. I am calling it the “canonical distribution” tool, because it analyzes the positional distribution of reads near genomic landmarks (such as splice sites, start/stop codons etc) of the UCSC “canonical” transcripts. Here’s an example:

Example Canonical Distribution

Using this tool requires that you run the RNA-Seq pipeline of version 1.6 or later. If you have data run through an older version of the pipeline, just upgrade your EP installation and re-run the pipeline (you should always save the invocation of the pipeline for just such an occasion). Of course it won’t redo the whole pipeline, just create the files missing, which are those necessary to generate the canonical distribution plots.

To get to the tool on the website, look under the “read_type” page. If you choose “positional” under the “readclass” dropdown menu then it will generate a canonical distribution plot. This option will be disabled on projects that don’t have the right files yet.

For more information, see the read types page of the User’s Guide.

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A web-based framework for analysis of RNA-Seq and microarray gene expression data