These are chat archives for dereneaton/ipyrad

Jan 2019
Jan 18 20:59 UTC
@isaacovercast I've had the same problem as @jhoepke and @caesantibanez. I'm running a few pair3rad assemblies on ipyrad v.0.7.28. Everything seems to go swimmingly until step 7. I can provide files and more details if it's helpful.
Jan 18 21:04 UTC
@isaacovercast One other question about results summaries from 3RAD-type data. In example below, is the count of refseq_mapped_reads the number of decloned reads that map to the reference? I'm trying to reconcile the difference between read_passed_filter and the sum of refseq_mapped_reads + refseq_unmapped_reads.
         state  reads_raw  reads_passed_filter  refseq_mapped_reads  refseq_unmapped_reads  clusters_total  clusters_hidepth  hetero_est  error_est
E18-423      4    1129858              1121394                79593                 375920            4656              3787    0.019173   0.001728
E18-424      4     496185               492755                50086                 184069            4621              3274    0.019523   0.002673