So I am aligning my RNA-seq using TopHat2 and STAR. STAR is a lot faster but the pipeline that my advisor uses is based on Tophat.
We are profiling expression levels of LINE-1 retrotransposon.
I would have to keep track of unmapped, multimapped, and uniquely mapped reads, and she advised that depending on the aligner, how this is done can vary.
But I am curious, if I use tools like RepeatMasker, would it matter which aligner I use?
To briefly describe our current pipeline, after aligning and deduping, we output multi-, unique, and unmapped bam files. And then merge multi/unmapped reads and realign it to a pseudogenome (using bowtie strata function). We get mapped repeat names, normalize reads, and group by element/family/class.
Thank you very much for your time and help!