Question: How to use mummer's output for visualization ?
0
gravatar for huiwenteh
8 months ago by
huiwenteh0
huiwenteh0 wrote:

Hi, I am using mummer for alignment and snp calling. Now I have my list of snps but I am stuck at this current step which is to visualize the coverage of the sequence. This is to confirm that the snps are really snps not some background noise or other factor. Any suggestion of visualization tool I can use by using mummer's output? p/s I am kinda new to bioinformatics, hopefully what I am doing is correct :) thank you

Best regards, huiwen

alignment • 379 views
ADD COMMENTlink written 8 months ago by huiwenteh0

Are you aligning reads? Why not use a tool more built for aligning reads and then outputs SAM/BAM so that you can just view coverage in genome browser?

ADD REPLYlink written 8 months ago by cmdcolin1.4k

I do recognize that mummer can output SNP, but probably other tools are easier to use

ADD REPLYlink written 8 months ago by cmdcolin1.4k
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