sseq_plot

Snakemake tool to make a depth plot of Strand-Seq data using the principles of composite files.

Installation

sseq_plot was developed with the following dependencies:

snakemake=7.32.4
R=4.2.0
ggplot2=3.3.6
dplyr=1.0.10
tidyr=1.2.1
readr=2.1.2
breakpointR=1.17.1

python=3.10.11
sys=3.10.11
gzip=3.8
os

Usage

sseq_plot is implemented as a Snakemake workflow.

1. Edit config/config.yaml:

   1. Point to your directory of mapped bam files
   2. Set the desired binsize (recommended: 10kbp)
   3. Link to a 'mappability' file which is part of ArbiGent.

2. run:

   Snakemake --cores 1

Output

Output plots can be found in res/[samplename]/pipe_plots/ and may look e.g. as follows, with orange and blue indicating the esimated copy numbers of forward and backward-facing seuqnece content. Regions with low mapping quality are shaded with grey background.