Strand-Specific Rna-Seq Alignment

Question

[Nicolas Rosewick]

Hi,

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.

Thanks,

N.

[Irsan]

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.

[Nicolas Rosewick]

I made a serach with "Strand-specific RNA-seq alignment" but nothing helpfull came out.

[Irsan]

Then Is Tophat The Only Mapper To Consider For Rna-Seq Data?

[Nicolas Rosewick]

ok great! thanks

[Malachi Griffith]

This post: Best Spliced Aligner To Human Genome With Limited Rna-Seq Reads also has many relevant answers

Answer 1

[Rohit]

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.

[Nicolas Rosewick]

I you use bowtie, better use tophat (which use bowtie) and is splice aware.