These are chat archives for dereneaton/ipyrad

Jan 2017
Jan 17 2017 06:48
@isaacovercast @dereneaton Hi guys, I have one question with the Assembly parameter 22 the "max_SNPs_locus". it is 20 by default, however, the loci of my dataset is only 44bp long. Should I reduce this parameter to, say 10 or 6 . Thanks a lot!
Deren Eaton
Jan 17 2017 14:53
@congliu0514 That sounds reasonable. Give it a try, and see if it removes many loci from your data set. Or, you can look at the _stats.txt output from step7 of your assembly to see a histogram showing the distribution of the number of SNPs per locus, which should give you a good idea of what would be a reasonable value for filtering.