These are chat archives for dereneaton/ipyrad

Apr 2018
Amanda Haponski
Apr 17 2018 14:04
@isaacovercast Hi Isaac, I have a question about the differences between ipyrad v0.6.17 and 0.7.17. I have a couple of different projects that I am working on for paired end ddRAD. I recently re-ran all of my data in v0.7.17 and ended up with ~400 loci less than from v0.6.17. My parameters were the exact same for both runs. Any ideas of why the difference?
Isaac Overcast
Apr 17 2018 14:52
@ahaponski_twitter Is it denovo or reference based? If you look in your output/*_stats.txt file right at the top it indicates the results of different filters applied, maybe there's a clue there? What was the average number of loci recovered per sample? 0.6.17 is quite old, the 0.7 version update was significant, and there have been a lot of minor bug fixes since then, so it's really hard to say what's causing the difference without really digging into the data. In the absence of other evidence I would suggest sticking with results from the most recent version.