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Splicing Efficiency Score Calculator

SE calculator extensively use Samtools for calculating the score. This script relies on "coordinates" and annotation file EXACTLY matching i.e. belongs to same genomic build and source.

This code can be used for both short and long reads

There are mainly 4 steps for SE score calculation

STEP 1 parse the input file and format for further analysis. Please uncheck "#" if you are using .GTF file

STEP 2 is optional if you are using the same genomic build (Mus_musculus.GRCm38.91.gtf) for querying genes. Please uncheck "#" if you are using new Ensembl_Genome.gtf file.

STEP 3 is the main step where all the stats will be computed for given Gene_list.bed

STEP 4 calculate the SE score by formula.

Usage:

sh Splicing_Efficiency_Calculator.sh <sample.bam> <Gene_list.bed> <Ensembl_Genome.gtf>

#Note: The formula needs to proofread/ re-implement again!