search

qasimyu / simuscop

a novel next-generation sequencing simulator using position and genomic contexts based error profiles
GNU General Public License v3.0
12 stars 4 forks source link

handling methylation sequencing data (e.g. whole-genome bisulfite) #2

Open bwlang opened 4 years ago

bwlang commented 4 years ago

I thnk that I could model non-methylated Cs as C->T SNPs and Gs as G->A SNPs , but the VCF will be VERY large. Since methylation sequencing is directional, I'll also have to do a second simulation without the C->T, G->A and mix original top and original bottom at 50%. You mentioned something about diplloid mode in your paper - maybe that could be used for this purpose too?

It might be helpful to provide a list of methylated Cs instead and get the simulator to produce the appropriate reads that way.

qasimyu commented 4 years ago

thank you for your interest in our work. We have not yet tested the tool to generate methylated data, we plan to try this direction in the future and complement this function.

gibberwocky commented 7 months ago

thank you for your interest in our work. We have not yet tested the tool to generate methylated data, we plan to try this direction in the future and complement this function.

I'd be interested in simulating methylation data also, so would be good to hear any progress on this.