Summerize R1 R2 read mapping direction and distance

Summary

To get a sense of how many mapped paired reads are +-, -+, –, or ++. This is mostly used for debug purposes.

Output

Two summerizing figures will be made, which were produced from: direction.summary.csv distance.summary.csv.

../../_images/paired_end_direction.png

Input

Need abs path to bam files

/path/to/R1.bam /path/to/R2.bam Banana
/path/to/R1.bam /path/to/R2.bam ABC
/path/to/R1.bam /path/to/R2.bam BCA
/path/to/R1.bam /path/to/R2.bam CBA

Usage

Go to your data directory and type the following.

Step 0: Load python version 2.7.13.

    hpcf_interactive

module load python/2.7.13

Step 1: Run the program

run_lsf.py -f input.list --pipeline_name summerize_R1_R2_mapping

code @ github.