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.
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