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Dear all,
Did anybody try to align genomic DNA using STAR (http://code.google.com/p/rna-star/)?
Thank you.
Did anybody try to align genomic DNA using STAR (http://code.google.com/p/rna-star/)?
Thank you.
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I know STAR is designed for RNA. But did anybody have any experience in aligning genomic DNA using STAR? -
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
AlexComment
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Hi Alex,
Thank you so much.
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