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Open Source Science

https://github.com/broadinstitute/zoonomia

Code related to 200 Mammals Project

https://github.com/broadinstitute/zoonomia

Science Score: 26.0%

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    Low similarity (5.0%) to scientific vocabulary
Last synced: 9 months ago · JSON representation

Repository

Code related to 200 Mammals Project

Basic Info
  • Host: GitHub
  • Owner: broadinstitute
  • License: mit
  • Language: R
  • Default Branch: master
  • Size: 48.8 KB
Statistics
  • Stars: 6
  • Watchers: 6
  • Forks: 4
  • Open Issues: 0
  • Releases: 1
Created over 6 years ago · Last pushed about 6 years ago
Metadata Files
Readme License

README.md

200Mammals

Code used in Zoonomia Project analyses

Diversity analysis (testing for correlations)

R script and input files for the diversity analysis in the Zoonomia paper

R script: diversity_analysis.correlation.R

Input files: (1) diversityanalysis.input.txt (2) diversityanalysis.pantheria.phenotypes.txt (3) diversityanalysis.pantheria.phenotypetypes.txt

Testing by regression with ordinal predictor for correlation of IUCN conservation status and SoH, heterozygosity: IUCN.diversity.correlation.R

Pipeline for calculating segments of heterozygosity from a mapped .bam file

Scripts adapted to run on an SGE/bash environment

paths are hardcoded in the scripts, matching directories need to be created

  1. Create a table of coverages per scaffold and discard anoumalous scaffolds:

qsub covanddisc.txt

  1. Calculate average heterozygosity and windowed heterozygosity per sample

qsub hetcalc.txt

  1. Calculate SoH per sample

for i in ls -1 ./50kb_scaffolds_het/; do cat ${i}|python3 mammals.py > ${i}".soh"; done

Owner

  • Name: Broad Institute
  • Login: broadinstitute
  • Kind: organization
  • Location: Cambridge, MA

Broad Institute of MIT and Harvard

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  • aserres (3)
  • elinorkarlsson (1)
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