/krispmer-expreminets

Codes of all experiments to prepare results are in this repository, along with comments

Primary LanguageRoff

krispmer-expreminets

Codes of all experiments to prepare results are in this repository, along with comments. This parent readme will also store directions and guidelines as well to recreate the experiments. Will also contain meeting notes.

Log in info

experiments are run in this machine: 131.215.78.41 ajker jonno

Installation tips

Had to do the following:

export PYTHONPATH=/home/atif/krispmer/soft/krispmer-github-repo/kRISP-mER/kRISP-meR_source:$PYTHONPATH
export PATH=/home/atif/krispmer/soft/bowtie2-2.4.5-linux-x86_64:$PATH
export PATH=/home/atif/guidescan2/guidescan-cli-master/build/bin:$PATH

Todo for the tool

  1. Add on-tgt activity scores
  2. Fix package error

Time to run on human genome:

Hamming distance = 3, time = ~14 sec, mem = 11.7 GB Hamming distance = 2, time = ~7 sec, mem = 0.64 GB Hamming distance = 1, time = ~6 sec, mem = 0.14 GB