README

Visualization of Intron Retention Data

Step 1: Obtain two different coverage bed files:
    1) Run: bedtools coverage -a "file containing introns" -b "bed file obtained by turning the SAM file after running HiSAT to BAM and then to bed using -bed12" -hist "coverage".bed
    2) Run: bedtools coverage -a "file containing each intron interval divided to 10 subinterval (10 lines per line in the file above)" -b "bed file same as above" -hist "entropy".bed
    
Step 2: run php main.php "coverage.bed" "entropy.bed"

Step 3: view plot.js, and replace the result file name with the corresponding result file (Lines 3 and 14).