#1 about pool size

[Anonymous]

Originally created by: elzedliu

Hi RoKofler,

Thanks for creating this beautiful software for the PopGen(omics) community.

I have a stupid question about the pool size in this commandline.
perl Variance-sliding.pl --input dmel.pileup --output dmel.pi --measure pi --window-size 10000 --step-size 10000 --min-count 2 --min-coverage 4 --max-coverage 400 --min-qual 20 --pool-size 500

Does 500 stands for number of individuals whose genomic DNA was mixed together and sequenced in a single lane or several lanes ?

Elzed

[Anonymous]

Originally posted by: RoKof... (code.google.com)@gmail.com

Sorry for the late response, I didn't see it any earlier....
Exactly, but you should propably use the chromosomes instead of individuals
2x500

best ro

[rrlove]

I would like to follow up on this issue. I don't know what changes to the software have been made since the original query; however, I see that the walkthrough on this site uses the number of individuals as the pool size, while the slides Dr. Kofler graciously posted from a class last year use the number of chromosomes. I've seen it done both ways in the literature.

What's the current recommendation?

Thanks.

[Robert Kofler]

no changes have been made, it's the number of chromosomes still. Thanks for pointing out this error in the walkthrough. I have to change this. Sorry for the confusion!
cheers ro