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alignment

Running bwa short read aligner on

find_ping_first_principles

Trying to find Ping locations by starting from basic first principles

find_ping_pong_jinfengpipeline

Directory for running Jinfeng's code for finding Ping. This directory is also found in the Rice_Rice_Baby team in the Stajich Lab github.

finding_ping_pong

Running two scripts (PickPing.py and PickPong.py) that use RelocaTE2 output to determine Ping and Pong locations.

github-fundamentals-nfmathieu94

github-fundamentals-nfmathieu94 created by GitHub Classroom

kickstart.nvim

My kickstart nvim configuration

make_simulated_genome

Code for building a simulated genome with insertions added and generating short read data. Directory is located in the Rice_Rice_Baby team in Stajich Lab.

mping_feature_intersect

A directory with code relevant to finding what genomic features mPing is landing in.

nvim-config

Configuration for nvim

relocate2_data_parsing

Project is designed around the manipulation of Relocate2 results. The goal is to have a place for code that is used to create combined insertion table.

relocate3

ReLocaTE code for identifying Transposons (TE) in genomes using re-sequencing data

relocate3_testing

Testing RelocaTE2 parts and parts that might be added.

sv_detection

Work relevant for detection of structural variation and their correlation to proximal mPings.

upsetplot