I am new to Bioinformatics and programming but can follow a clear program in order to arrive at my result.I have a deadline task in alignment of reads.
I used, Rsubread, HISAT2 and STAR to align 15 million paired simulated data and I got results in BAM file for STAR and Rsubread but SAM format for HISAT2. I will like to know the if the splice junction files have alignment that is the same as in the annotated file and I used hg38 build 2. In other words, I want to know the true or correct splice junctions. As I said earlier, I am new to this. I already have the Rsubread bed file, HISAT2 text file and the SJ.out.tab file from STAR.
What I want to find out is the number of correct splice junctions in each result? How can I go about this? Does anyone have a script I can use or a software that can help me?
Another question, is that I want to know the splice junctions that are common to the aligners AND the ones that are unique to each. Maybe a script that can produce this result in Venn diagram.
Thanks for your response to help a newbie bioinformatician.