Xiaoqing Yu, Kishore Guda, Joseph Willis, Martina Veigl, Zhenghe Wang, Sanford Markowitz, Mark D Adams and Shuying Sun*
Corresponding author: Shuying Sun firstname.lastname@example.org
BioData Mining 2012, 5:6 doi:10.1186/1756-0381-5-6
(2013-03-13 15:29) Novocraft Technologies
Your paper shows a high false positive rate for alignments from Novoalign and I'm
wondering if this could just be an effect of the soft-clipping in Novoalign. Novoalign
will soft-clip alignments that have mismatches near the ends of the reads and this
results in a shift in position of the alignment compared to the simulated alignment
location. Depending on the version of Novoalign you used you might get 3-4bp soft-clipped
off a read when the mismatch is in the first/last 3-4bp of the read. This could lead
to 6-8% false positive alignments (in 50bp reads) if you don't allow for soft clipping
in your evaluation.
Could you comment on this?
Would it also be possible for you to provide more details regard the version of Novoalign
that you used and provide access to data and scripts that you used.
Director of Novocraft Technologies, commercial interest in Novoalign
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