align genomic DNA using STAR

[tong liu]

Hi all,

I know STAR was designed to align RNA. But did anybody use it as a DNA-aligner for genomic DNA?

Thank you.

Tong

[Alexander Dobin]

STAR was designed for aligning RNA-seq data, and is not optimized for DNA-seq mapping. In particular, the "mapping" quality values are naively defined and may give you trouble with SNP callers. Some users had managed to obtain decent results with STAR, see this post and the comparison on bioplanet within it. You can see that STAR's accuracy is slightly better than Bowtie2's, but not as good as BWA's. STAR advantage is very high speed.

To map DNA data you would need to prohibit splicing with:
--alignIntronMax 1 --alignMatesGapMax <MaxInsertSize-2*ReadLength>.

Cheers
Alex 

[Felix Schlesinger]

If you are looking for a large-memory / high-speed DNA short read aligner, Isaac might be an option:

http://bioinformatics.oxfordjournals.org/content/early/2013/06/04/bioinformatics.btt314

Otherwise BWA-Mem is probably the best default choice.

  Felix

[Jason Knight]

Also another choice is SNAP:

http://snap.cs.berkeley.edu/

Although they still don't have anything more than an arxiv paper on it (with impressive looking results). 

[tong liu]

Thank you everybody.

Tong