UPDATE: due to security concerns, I’ve had to make the server where we’ve been serving up data non-public. I’m in the process of unloading many of these data sets to Google Drive, and will update links accordingly. In the mean time, send me (KRT) and email, and I’ll prioritize getting what you need back online.
This page lists sequence data, alignments, etc., resulting from lab publications. A lot of our ouptut is software, which you can find at our software page.
GFF files from Rogers et al. (accepted) Revised annotations, sex-biased expression, and lineage-specific genes in the Drosophila melanogaster group G3. The accession numbers for the RNA-seq data are PRJNA196536, PRJNA193071, PRJNA257286, and PRJNA257287.
Supplementary material from Rogers et al. (2014) Landscape of tandem duplication in Drosophila yakuba and Drosophila simulans. Please note: the BED files for D. simulans are based on the w501 reference genome, hosted at Peter Andolfatto’s website. If you plug our BED files into the UCSC browser, you’ll be quite a bit off in terms of coordinates, as they are still using the Begun et al. reference.
Code from Baldwin-Brown, Long, and Thornton (2014) Mol Biol Evol is on Thornton’s github repository.
Simulation code and output from Thornton, Foran, and Long (2013) Properties and Modeling of GWAS when Complex Disease Risk is due to non-complementing, deleterious mutations in genes of large effect. PLoS Genetics 9: e1003258.
There are several resources from from Cridland, MacDonald, Long, and Thornton (2013) Abundance and Distribution of Transposable Elements in two Drosophila QTL Mapping Resources. Molecular Biology and Evolution. Manuscript. These resource are:
NOTE (Nov. 17, 2014): the pipeline code linked to below is being re-implemented. Please keep track of the pecnv package, which will integrate our existing CNV-calling code from PE mapping with the TE calling pipeline. The current “dev” branch of that repo re-implements the presence/absence part of the pipline in a more streamlined manner. This code will eventually become release pecnv-0.1.4.
UPDATE Nov. 21, 2014): pecnv version 0.1.4 is released, and replaces numbers 1 and 4 in the list below with a C++ reimplentation of the presence/absence calling software.