Local Alignment Of Rna-Seq Data

Question

[Nicolas Rosewick]

Hi,

Anyone knows a good tool to align RNA-Seq data in local alignment mode ? The tool has to be splice-aware. Example (in red: aligned nucleotides , in gray, soft-clipping )

Thanks

N.

[Rohit]

I don't actually understand what you mean by local alignment mode..

But I think Tophat2 does the mapping keeping in mind the splice variants.

You can use subread too http://subread.sourceforge.net/