Skip to content

This repository contains the prebuilt models for BIRD.

Notifications You must be signed in to change notification settings

WeiqiangZhou/BIRD-model

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

16 Commits
 
 

Repository files navigation

This repository contains the prebuilt models for BIRD.

BIRD prediction models for human reference genome hg38

  1. RNA-seq model based on FPKM, current release (trained with 174 ENCODE samples): https://github.com/WeiqiangZhou/BIRD-model/releases/download/v1.4/human_hg38_model.bin.zip

BIRD prediction models for human reference genome hg19

There are four models available for hg19:

  1. RNA-seq model based on FPKM, current release (trained with 167 ENCODE samples): https://github.com/WeiqiangZhou/BIRD-model/releases/download/v1.3/human_hg19_model.bin.zip

  2. RNA-seq model based on FPKM, previous release (trained with 70 Epigenome Roadmap samples): https://github.com/WeiqiangZhou/BIRD-model/releases/download/v1.2/RNAseq_model_file.bin.zip

  3. RNA-seq model based on FPKM for 2 million loci, previous release (trained with 70 Epigenome Roadmap samples): https://github.com/WeiqiangZhou/BIRD-model/releases/download/v1.0/RNAseq_model_file_2M.bin.zip

  4. Exon Array model: https://github.com/WeiqiangZhou/BIRD-model/releases/download/v1.1/Exonarray_model_file.bin.zip

How to use

  1. Download and unzip the required model from this repo. For prediction based on RNA-seq data, we suggest users use the current release.
wget https://github.com/WeiqiangZhou/BIRD-model/releases/download/v1.3/human_hg19_model.bin.zip
unzip human_hg19_model.bin.zip

You will get the model file: human_hg19_model.bin.

  1. Install BIRD using the source code.
wget https://github.com/WeiqiangZhou/BIRD/archive/master.zip
unzip master.zip
cd BIRD-master
make
  1. Prediction using the model file.

Suppose you store the model files in path_to_model and install BIRD in path_to_BIRD.

Run:

path_to_BIRD/BIRD_predict -b path_to_model/human_hg19_model.bin -i FPKM_data_matrix.txt -o output_file.txt

More instructions for BIRD can be found in https://github.com/WeiqiangZhou/BIRD