Question: copy number profiling from shallow sequenzing or whole genome low coverage seq for mouse genome
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gravatar for ifudontmind_plzz
5.0 years ago by
Netherlands
ifudontmind_plzz150 wrote:

I am curious to know if there any available tools for analysing the copy number variation of mouse data generated from shallow-seq or whole genome low coverage seg. 

 

sequencing next-gen • 1.5k views
ADD COMMENTlink modified 4.9 years ago by Eric T.2.6k • written 5.0 years ago by ifudontmind_plzz150

Are these tumor/normal samples, or simply from a population?

ADD REPLYlink written 5.0 years ago by Sean Davis26k

@Sean , i have only mouse tumor samples

ADD REPLYlink written 5.0 years ago by ifudontmind_plzz150
2
gravatar for Eric T.
4.9 years ago by
Eric T.2.6k
San Francisco, CA
Eric T.2.6k wrote:

You could use CNVkit on your dataset. I recommend making a BED file of the full-length genes of interest in the genome -- preferably non-overlapping, probably using bedtools; no need to be comprehensive, but you can if you like. Then run CNVkit with equal "target" and "antitarget" bin sizes, aiming for about 200-300 reads per bin, e.g. 10000 bp for 0.5-fold coverage.

ADD COMMENTlink written 4.9 years ago by Eric T.2.6k
1
gravatar for bruce.moran
5.0 years ago by
bruce.moran790
Ireland
bruce.moran790 wrote:

You can use the QDNAseq package in Bioconductor, pretty straight forward to get running if you can use R.

ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by bruce.moran790
0
gravatar for ifudontmind_plzz
5.0 years ago by
Netherlands
ifudontmind_plzz150 wrote:

@bruce, i doubt QDNAseq is tailored for only human genome not for mouse

ADD COMMENTlink written 5.0 years ago by ifudontmind_plzz150

Sorry, you are correct. You could make your own annotation but that will not be as straight forward...

ADD REPLYlink written 5.0 years ago by bruce.moran790
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