Processed loci from Cufflinks

Question

[Munmun]

I'm running Cufflinks from the output of TopHat as well from the output of HISAT2 and Bowtie2-align. The number of processed loci are highly variable for all the outputs. This further affects the .gtf output files.

I want to know what might be the reason for difference in the results when using different aligners. And what should be done to avoid this. Any idea please let me know..

[Amitm]

Hi, All the three aligners mentioned are very different. I am assuming that this is RNA-sequencing data (from an eukaryotic organism) in which case splice-aware aligners are supposed to be used like TopHat, HISAT2, STAR etc. Bowtie2 is for aligning DNA sequencing reads and hence a not a good choice for RNA. Unless your motive is to compare tools and their nitty-gritty, choose any one splice-aware aligner and use its BAM output for Cufflinks. TopHat and HISAT2 have quite different approach to alignment and hence it is expected to see difference in Cufflinks output.