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plotCoverageExons.py

Plot the coverage at some specific region from multiple bam files:

./plotCoverageExons.py [-p <geneposition>] [-o <outfile>.pdf] [-options] <bamfile1> [<bamfile2> ...]

This grew over time, please excuse the bad code

  • Uses pysam to get pile up reads covering the selected regions
  • Plots the coverage using matplotlib
  • Allows grouping of samples and other customization

Example

example

Full usage

./plotCoverageExons.py [-p <geneposition>] [-options] <bamfile1> [<bamfile2> ...]

-p <geneposition>          specify genomic position with: <chromosome>:<start>-<end>
-z <sizefactor1>,<sf2>,... specify normalization size factors for each bamfile in order
-s <+|->                   specify strand ( + or - ) to be included in plot title
-e <start>-<end>,<s-e>,... select feature regions to be plotted exclusively
-l <label1>,<l2>,...       specify labels for the regions
-c <condition1>,<c2>,...   specify patterns to group bamfiles by filename
-n <name1>,<n2>,...        specify names for the condition groups
-u <uname>                 include unmatched bamfiles under name <uname>
-a                         average samples of the same condition, default off (plot all samples)
-L                         set logarithmic scale for the y-axis
-S                         add smoothed curve (rolling mean of 49-mers, twice applied)
-f                         enable samtools-like filtering of reads (default no filtering)
-o <file>                  specify output filename and thus output format
-P <file>                  only write coverage data to pickle file

Dependencies

  • python
  • matplotlib
  • numpy
  • pysam

This list is potentially incomplete.

Create a conda enviroment

conda env create --file ./plotCoverageExons.yaml
conda activate plotCoverageExons