analysis of the Timema single generation experiment-21viii13 - Aug 21, 2013 11:1:5 PM
bgsr software, bug fixes-27viii13 - Aug 27, 2013 11:13:13 PM
bgsr, new test with simulated data-29viii13 - Aug 29, 2013 6:4:48 PM
bgsr test take two-29viii13 - Aug 29, 2013 11:15:13 PM
bgsr working? ready to run with Timema data-29viii13 - Aug 30, 2013 7:59:28 PM
timema bgsr analysis running on rc-29viii13 - Aug 30, 2013 8:28:25 PM
timema bgsr, take two-2ix13 - Sep 02, 2013 7:34:18 PM
timema bgsr take three-4ix13 - Sep 04, 2013 5:39:1 PM
initial results for bgsr - Sep 25, 2013 7:31:12 PM
bgsr mostly done running - Oct 08, 2013 3:30:49 PM
revisions for within generation transplant experiment, Aaron's trait associated snps - Oct 10, 2013 3:21:44 PM
stripe-associated SNPs and allele frequency change, within-generation transplant experiment - Oct 11, 2013 5:12:4 PM
selection on adenostoma - Oct 16, 2013 3:11:8 PM
LD for exceptional change SNPs - Oct 16, 2013 8:49:11 PM
processing whole genome sequences from the ecology letters experiment - May 07, 2014 3:29:52 PM
compressing, sort and index genomes - May 07, 2014 8:33:35 PM
merging alignments and assigning ids - May 09, 2014 3:48:0 PM
variant calling, within generation experiment whole genome sequences - May 11, 2014 10:52:52 PM
error, re-running alignments, etc. - Jun 16, 2014 7:11:32 PM
variant filtering and genotype estimation for within generation whole genome sequences - Jun 23, 2014 8:3:55 PM
removing PCR duplicates - Jun 23, 2014 8:5:46 PM
preparing a genome for GATK - Jun 23, 2014 9:35:12 PM
read group header, more problmes - Jun 24, 2014 11:2:18 PM
GATK-friendly processing continued - Jun 26, 2014 7:21:44 PM
found missing individuals - Jun 26, 2014 7:52:31 PM
pcr duplicates - Jun 27, 2014 3:34:22 PM
indel realignment - Aug 08, 2014 5:5:46 PM
variant calling with GATK unified genotyper - Aug 08, 2014 10:58:22 PM
variant calling continued - Aug 13, 2014 2:42:2 PM
variant filtering 500 genomes - Aug 19, 2014 11:39:0 PM
timema 500 genomes, extracting genotype likelihoods - Aug 20, 2014 3:43:29 PM
500 Timema genomes, genotype point estimates - Aug 20, 2014 9:38:52 PM
initial gemma analysis with 500 (491) timema genomes - Aug 22, 2014 3:39:0 PM
timema genomes, gemma probit model - Aug 22, 2014 7:8:55 PM
timema genomes, gemma results and next attemps - Aug 25, 2014 10:23:53 PM
timema genomes LMM - Aug 27, 2014 2:29:24 PM
LMM results and thoughts - Aug 28, 2014 10:5:20 PM
gemma, 500 genomes, BSLMM probit model with maf > 5% - Aug 28, 2014 10:9:31 PM
more thoughts on gemma analyses - Aug 29, 2014 5:32:17 PM
the significant SNP - Aug 30, 2014 11:4:17 PM
rerunning the T. crisinae 500 genome alignments again - Sep 26, 2014 8:57:41 PM
re-running compression and sorting on 500 genomes - Oct 01, 2014 9:36:36 PM
recalling variants with GATK on the 500 genomes - Oct 02, 2014 3:17:14 PM
filtering new 500 genome variants - Oct 19, 2014 9:57:42 PM
gemma = fail - Nov 02, 2014 9:20:44 PM
pimass on experimental genomes to estimate no. snps and pve - Nov 02, 2014 9:23:19 PM
initial pimass results - Nov 03, 2014 3:23:56 PM
pimass, continued - Nov 17, 2014 3:30:39 PM
dumb problems - Nov 19, 2014 5:24:24 PM
~100 pimass runs, almost there - Nov 25, 2014 4:44:6 PM
pimass, 500 genomes, minimum MAF 5% - Nov 25, 2014 4:54:6 PM
sanity check on timema 500 genomes - Dec 12, 2014 11:13:51 PM
mapping stripe in timema 500 genomes - Dec 15, 2014 8:26:3 PM
stripe != survival - Dec 17, 2014 12:3:59 AM
500 genomes, het. vs. survival correlation - Dec 24, 2014 10:50:59 PM
association between Fst and GWA effects, whole genomes - Jan 09, 2015 8:29:9 PM
gemma with GBS data from Ecology Letters - Jan 20, 2015 8:20:18 PM
re-running alignment and variant calling with the ecology letters GBS data - Feb 08, 2015 4:1:7 AM
Diversity and differentiation between A and C treatment for the OGA between generation experiment - Jan 08, 2017 3:10:28 AM