These are chat archives for dereneaton/ipyrad

Nov 2017
Jean-RĂ©mi Trotta
Nov 23 2017 09:02
Hi! I would need a clarification about the final stats file in the outfiles folder. I run ipyrad as denovo-reference (chloroplast ref.) and when I look at those metrics I see that for example, for a sample, I have 805,763 raw reads, 801,554 passing filters, 4,841 mapping to the reference ("refseq_mapped_reads") but only 553,120 unmapped. So my question is: why mapped reads + unmapped reads is not equal to passing filters reads? From what I understand, using this assembly method, I would expect to discard the 4,841 reads mapping to the choloroplast sequence and used the 796,713 (801554-4841) remaining reads for the denovo assembly.
Ollie White
Nov 23 2017 15:58

Hi @dereneaton @isaacovercast, I've been doing some abba-babba test using the API. The output plot for the analyses is hard to interpret simply because I have a large number of individuals in the backbone phylogeny. See attached photo above

Most of the text is overlapping unfortunately. How would you go about formatting the plot smaller? Or would it be possible to create a a table of results where the tree for each row was also included? Perhaps something like:

    dstat    bootmean    bootstd    Z    ABBA    BABA    nloci   tree
0    -0.099    -0.097    0.043    2.311    258.844    315.438    6718    P4: SampleA, P3: SampleB, P2: SampleC, P1: SampleD   
1    -0.114    -0.115    0.039    2.886    303.938    381.906    8221    P4: SampleA, P3: SampleB, P2: SampleC, P1: SampE