These are chat archives for dereneaton/ipyrad

Apr 2017
Apr 05 2017 02:46
@isaacovercast Hi, I'm interested in ABBA/ABAB test in ipyrad, how can I get the cookbook or tutorial? Can I use the output .loci file from ipyrad for pyrad D-statistics test analyses. because pyrad takes too long for assembly, I tryed to change the form of the .loci files from ipyrad as with the pyrad, when the assembly only include 4 samples, I succeed to get the results, but I'm worry that is it make sense to manage like this way.
Isaac Overcast
Apr 05 2017 07:43
@R2C2_Lab_twitter I actually just figured out what was going on yesterday and am in the process of testing the fix. Could be ready in the next day or two. The problem is that there is a special character in the scaffold names in your reference sequence. This character "|" causes bad problems during the assembly, it has special meaning to the bash shell, so it makes things go kind of nuts. A quick fix workaround is to find and replace all instances of "|" in your reference sequence with "_". That would 100% fix the problem.
Apr 05 2017 10:23
@isaacovercast great news! Maybe it’s better if I wait for you to fix it (in the next update?) instead of replacing all pipe signs in the reference sequence
Apr 05 2017 21:47
@isaacovercast @dereneaton Hi! One question. What is the difference between the heterozygosity reported in step 4 and the one reported in step 5? Is that in step 5 the same as the individual nucleotide diversity (pi)?