Coverting physical location (bp) to Mbp

[Rachel Tavares]

Hello!

I am working with rice genotyping by sequencing data that gives position in basepairs. I have over 93,000 markers so it is very dense and I believe I can convert into mbp and it will be accepted by the program. Is there any function that can do this conversion easily? Converting all 93,944 markers from bp to mbp will not be a small task.

I would rather avoid making an assumption on recombination rates etc.. for the conversion of bp to cM which I know some have assumed this rate is ~273kb per cM in rice. 

Thank you for any input!

Rachel Tavares

[Karl Broman]

You can load it into R/qtl with positions in basepairs, and it will give a warning, but there shouldn't be an error that will prevent you from working with the data.

You can then use the function rescalemap() to rescale the positions from basepairs to Mbp, or to rescale them to estimated cM.

Scaling 273 kbp per cM means scaling 1 Mbp to (1/0.273) cM

mycross_Mbp <- rescalemap(mycross_bp, scale=1e-6)

mycross_cM <- rescalemap(mycross_Mbp, scale=1/0.273)

karl

[Rachel Tavares]

Thanks Karl! I did receive the warning and that's what made me realize the mistake.