These are chat archives for dereneaton/ipyrad

Dec 2017
Isaac Overcast
Dec 01 2017 13:37
@jrtrottablanc The first stage of step 3 is dereplication, which simply collapses all identical sequences. The discrepancy between reads passing filter and refseq unmapped reads is due to this dereplication. The counts of all duplicate loci are retained and used downstream, but they aren't recorded in this simple metric. Hope that helps.
Isaac Overcast
Dec 01 2017 13:48
@DylanHCohen_twitter What are you trying to do to the nexus file ipyrad already writes out? I know people who have used the ipyrad output with SNAPP and it worked fine.
Dec 01 2017 14:13
@isaacovercast @dereneaton I found that the command -m was very useful! Now, I separate my data to several pools and run step 1-4 respectively. Subsequently, I want to merge all the assemblies to a new one and then run step 5-7. Also, I detected the different flows with the same small database and got the same results. But I want to know if I run a very big dataset in this way, it will get the same result comparing with pooling the data together?
Dec 01 2017 23:43
@isaacovercast I am trying to infer species trees using SNAPP and BPP. From what I understand SNAPP does not work well with missing data. So I am trying to use Phyrnomics to modify my .phy data set. Basically I want to use Phyrnomics to remove non binary sites, pull out a single snp from each locus, and translate bases to appropriate coding. There are some recent papers that suggest using Phyrnomics to do this, and use pyrad output files to start with. I am wondering if the .phy files differ between ipyrad and pyrad? Is it possible to get an unlinked snps file from ipyrad? The sample input data sets are unlinked...