Local Alignment Of Rna-Seq Data

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 )

enter image description here

Thanks

rna-seq local alignment

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written 12.9 years ago by Nicolas Rosewick

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/

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written 12.9 years ago by Rohit

0 answers

No answers yet.

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