Question: identifying recombination events
0
gravatar for an_nguyen2489
8 months ago by
an_nguyen24890 wrote:

Hi everyone,

I am totally new with whole-genome sequencing, coding and analysis. I am now handling with huge amounts of sequencing data which I need to map reads of evolved and donor strains with the reference genome to identify recombination events, including long fragments and SNPs. I also need to differentiate between de novo mutations with SNPs transferred from donors to recipients. I need to calculate the average length of imports as well.

I had the list of mutations generated from the comparison between ref genome with donors, and ref genome with evolved strains. I can do the comparison again by using excel, but It is really handy and time-consuming. Does anyone have experience doing with this field? Any faster method to deal with this complicated analysis?

Thank you.

sequencing next-gen • 182 views
ADD COMMENTlink modified 8 months ago by genomax80k • written 8 months ago by an_nguyen24890

ClonalFrameML would be a good place to start if you have data for entire genome assemblies.

ADD REPLYlink written 8 months ago by Joe16k

I used the whole population sequencing instead of clone.

ADD REPLYlink written 8 months ago by an_nguyen24890

That’s not what I was getting at. Do you have whole genomes for all of the organisms of interest, or just amplicon sequencing for example?

ADD REPLYlink written 8 months ago by Joe16k
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