STAR vs HISAT2 comparison RNA-Seq reads

Question

[wheelz540]

Hi,

I have bam files generated by HISAT2 and STAR. I want to compare the results of both aligners. What parameters should i look at ?

[GenoMax]

I want to compare the results of both aligners.

In terms of what (accuracy/reproducibility)? You may need to do some downstream analysis as there is not much there to compare with alignment files. You may be able to say x reads aligned with STAR but y with HISAT2.

Perhaps you can use this paper.