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Removed very old comment about alleles format in the faq
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isaacovercast committed Apr 11, 2024
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Expand Up @@ -160,19 +160,6 @@ I know that people have also used stacks (because stacks treats r1 andr2 as inde
loci). If people ask me how to denovo assemble with PE-RAD in ipyrad I tell them to
just assemble it as SE and ignore R2.

Why doesn't ipyrad write out the .alleles format with phased alleles like pyrad used to?
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We're hoping to provide something similar eventually, the problem with the pyrad alleles
file is that the alleles are only phased correctly when we enforce that reads must align
almost completely, i.e., they are not staggered in their overlap. So the alleles are
correct for RAD data, because the reads match up perfectly on their left side, however,
staggered overlaps are common in other data sets that use very common cutters, like
ezRAD and some GBS, and especially so when R1 and R2 reads merge. So we needed to change
to an alternative way of coding the alleles so that we can store both phased and unphased
alleles, and its just taking a while to do. So for now we are only providing unphased
alleles, although we do save the estimated number of alleles for each locus. This
information is kind of hidden under the hood at the moment though.

Why is my assembly taking FOREVER to run?
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There have been a few questions recently about long running jobs (e.g., >150 hours), which
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