Question: Why alignment in "blat" and "nucmer" are different?
gravatar for Yuyayuya
3.0 years ago by
Yuyayuya170 wrote:

Hello everyone,

I'm doing genome assembly using SOAPdenovo2-MUMmer3 pipeline. After scaffolds were built, I used nucmer to align each scaffold to chromosome based on the reference genome.

After nucmer alignment, Scaffold18596 is located in chr.5 (only 530 bp match chr.5 but it's the highest score). However, if I simply blat the sequence of Scaffold18596 to the same reference genome, I found there're several perfect matches in chr.1 (11,360 bp, 3,618 bp, 2,445 bp).

In this case, why nucmer gave me this strange result? For the command, I just simply used nucmer -p <Reference> <Query>

Thank you!

alignment assembly • 724 views
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