Question: Best practice to identify Copy number alteration from mouse whole genome low coverage sequencing study
2
gravatar for ifudontmind_plzz
4.7 years ago by
Netherlands
ifudontmind_plzz130 wrote:

Hi,

What could be the better tool to identify copy number  alteration of mouse whole genome low coverage sequencing study (BAM file)? 

sequencing next-gen • 1.6k views
ADD COMMENTlink modified 4.4 years ago by h.mon27k • written 4.7 years ago by ifudontmind_plzz130

What do you mean by "best way"? Is it what tool to use? If so, there were many such questions here on biostars: Recommendation For Cnv Calling Program Based On Depth Of Coverage From Bam

ADD REPLYlink written 4.4 years ago by PoGibas4.8k

@Pgibas, Yes i mean tools. Thank you

ADD REPLYlink written 4.4 years ago by ifudontmind_plzz130

Is it a inbred strain? If yes, you can try https://www.sanger.ac.uk/resources/software/cnd . It has been specifically designed for the inbred strains but I am not sure how it will perform for a low coverage study. 

ADD REPLYlink written 4.4 years ago by Ashutosh Pandey11k

it is not purely a  inbred strain. 

ADD REPLYlink written 4.4 years ago by ifudontmind_plzz130
0
gravatar for h.mon
4.4 years ago by
h.mon27k
Brazil
h.mon27k wrote:

This paper claims to have the most accurate method to detect CNV from low-coverage sequencing. I am halfway through it and did not find link to sources / executables. And of course, always take with a grain of salt non-independent software comparisons. Their introduction cites a bunch of other software as well.

ADD COMMENTlink written 4.4 years ago by h.mon27k
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