Update: visualize gene body coverage of multiple RNA-seq samples

[Liguo Wang]

RSeQC v2.4 update:
Rewrite “geneBody_coverage.py”

1) Memory-efficient: RAM consumption < 100M

2) Flexible input to handle one or more BAM files:

*Input a singel BAM file.
    Example: geneBody_coverage.py -r hg19.housekeeping.bed -i test.bam -o output

*Input several BAM files (separated by ”,”)
    Example: geneBody_coverage.py -r hg19.housekeeping.bed -i test1.bam,test2.bam,test3.bam -o output

*Input plain text file containing the path of BAM file(s).
    Example: geneBody_coverage.py -r hg19.housekeeping.bed -i bam_path.txt -o output

*Input a directory containing BAM file(s).
    Example: geneBody_coverage.py -r hg19.housekeeping.bed -i /data/alignment/ -o output

3) If 3 or more BAM files were provided. This program generated a lineGraph and a heatmap (see attached examples). If less than 3 BAM files were provided, only lineGraph was generated.

4) When heatmap was generated, samples were ranked by the “skewness” of the coverage: Sample with best (worst) coverage will be displayed at the top (bottom) of the heat map.

5) Coverage skewness was measured by Pearson’s skewness coefficients


http://rseqc.sourceforge.net/