gwct / mus-t-haplotype

Mus t-haplotype phylogenies

This repository contains all scripts and data files associated with the Mus t-haplotype project

Workflow outline

Briefly, the workflow was:

1. Download genomes
2. Extract t-haplotype homologous chromosomes
3. Mask chromosomes
4. Align chromosomes with Cactus
5. Convert to MAF and FASTA alignments
6. Partition alignments in windows across the chromosome (10kb)
7. Filter alignments
8. Make window trees with IQ-tree
9. Count topologies

For more detailed, step-by-step instructions see notes.txt.

Files

Folder	Description
analysis/	All raw input, intermediate, and raw output files from all steps of the workflow -- NOTE: This folder and all its sub-folders are excluded from the github repo due to size limitations
analysis/00-genomes/	The raw and masked FASTA sequences for the selected genomes
analysis/01-cactus-all-mask/	The output sequences and HAL file from Cactus
analysis/02-mus-t-windows/	The input, intermediate, and raw output files for the windowed phylogeny analyses
analysis/02-mus-t-windows/00-maf-rmdups/	The Cactus alignment in MAF format (converted from HAL), with mm10 as the reference
analysis/02-mus-t-windows/01-bed-windows/	Bed files that partition the input chromosome (chr17) into 10kb windows
analysis/02-mus-t-windows/02-fasta/	FASTA files for the alignments of each 10kb window, extracted from the MAF
analysis/02-mus-t-windows/03-fasta-no-anc-filter/	FASTA files for the alignments of each 10kb window with the ancestral sequences removed and gappy sites filtered
analysis/02-mus-t-windows/04-iqtree/	Raw IQ-tree and ASTRAL output files, including window trees, a concatenated species tree, and an ASTRAL species tree
analysis/02-mus-t-windows/mus-t-haplotype-6.hal	The final HAL output file from Cactus, copied over from analysis/01-cactus-all-mask/
data/	Processed summary files from the analyses
data/cactus-stats.csv	Output from halStats, which summarizes the Cactus alignment
data/cactus-summarize.csv	Output from halSummarizeMutations, which counts inferred mutations in the Cactus alignment
data/genomes.txt	The tree and paths to the genomes for input to Cactus
data/mm10-10kb-spec-counts.tsv	The counts of each species in the final 10kb window alignments
data/mm10-10kb-topo-counts.csv	The counts and inferred topologies for the 10kb window alignments
data/mm10-10kb-window-stats.tsv	Alignment stats for filtering of the 10kb window alignments
data/mus-t-haplotype-cactus.tre	The tree used as input for Cactus in Newick format
data/samples.csv	Information on the input genomes
docs/	Scripts for analyzing the data files and generating HTML reports for the web
figs/	Figures
scripts/	All scripts and config files used in the workflow
notes.txt	Detailed, step-by-step instructions for the workflow
README.md	This file!