From 255f647d8283366331c847ffe647b426dd181525 Mon Sep 17 00:00:00 2001 From: Isaac Overcast Date: Thu, 11 Apr 2024 11:22:35 -0400 Subject: [PATCH] Removed very old comment about alleles format in the faq --- newdocs/faq.rst | 13 ------------- 1 file changed, 13 deletions(-) diff --git a/newdocs/faq.rst b/newdocs/faq.rst index 5ea038d6..53b2f111 100644 --- a/newdocs/faq.rst +++ b/newdocs/faq.rst @@ -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? ----------------------------------------------------------------------------------------- -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? ----------------------------------------- There have been a few questions recently about long running jobs (e.g., >150 hours), which