Is there a list of strand-specific RNA-seq aligners ? For now I use tophat 2 with strand-specific parameter but I want to try other tools.
Have you tried to search for related questions at biostars? Questions are conveniently categorized by tagging them. This way, the tag RNA-seq includes 162 threads, many of them discussing alignment.
I made a serach with "Strand-specific RNA-seq alignment" but nothing helpfull came out.
Then Is Tophat The Only Mapper To Consider For Rna-Seq Data?
ok great! thanks
This post: Best Spliced Aligner To Human Genome With Limited Rna-Seq Reads also has many relevant answers
Dissect is another tool for alignment.
Bowtie works fine but for RNA-seq you might get many unaligned reads as it does not support alternative splicing, go for the --local option with less stringency.
I you use bowtie, better use tophat (which use bowtie) and is splice aware.