Most of the recent codes and applications from Gokcumen Lab can be found in our GitHub page: https://github.com/GokcumenLab
Previous work can be found individually as shown here:
The joint genotypic file for the nine genomes that we sequenced + 1 additional genome for quality check for genotype calling:
2 CEU (one of them [NA12878] is used for quality-check)
You can reach the data here.
The mapped RNAseq files can be reached from the GEO database here. If it is needed urgently, please contact gokcumen@gmail.com as this data is currently marked as “private” and is scheduled to be released on Mar 31, 2017.
You can reach the codes and input files here.
You can reach the codes and input files here.
XU ET AL. (Under Review)
You can reach the data and codes here.
VCFtoTree can be accessed here.
You can reach the data here and R codes here.
VCFtoTree can be accessed here.
You can reach the data here, and R codes here.
VCFtoTree can be accessed here.
Tabulated 1000 Genomes deletion calls and their allele frequencies (input file for the R analysis, also can be opened by excel).
.bed file for the 1000 Genome deletions (input file for Galaxy)
perl code for converting .vcf files to .fasta files (Courtesy of Pavlos Pavlidis)
Frequencies of KAP gene (input file for the R analysis – graph)
R code for subsetting and graphs
You can reach the codes here
Buffalo Evolutionary and Anthropological Genomics Laboratory (BEAGL) 
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