RNAnorm

Normalization of RNA-seq expression counts

Supported methods:

• Counts per million (CPM)
• Fragments Per Kilobase of transcript per Million mapped reads (FPKM)
• Transcript per kilobase million (TPM)

Filtering for coexpression network construction such as WGCNA

• MADs
• coefficient of variation (CV)

Dependencies

1. gcc 4.8+ or clang 3.4+
2. cmake 3.2+

Getting start

git clone https://github.com/lyd0527/RNAnorm.git
cd RNAnorm; make

Usage: RNAnorm <OPTION>

Option:

	-i 	raw count maxtrix from featureCount or HTSeq
	-o 	output prefix
	-f 	filtering or not [off]
	-v 	minimum threshold value of MAD or CV [0.01]
	-m 	method: CV or MAD [CV]

Input Format

GeneID	Length	Sample1	Sample2	Sample3	Sample4
g1	100	23	13	1	3
g2	150	3	4	1	3
g3	120	4	10	23	3
g4	145	10	3	4	5

Examples:

Count2FPKM/TPM

./RNAnorm -i count.input -o output_prefix

Count2FPKM/TPM + Filtering (CV method)

./RNAnorm -i count.input -o output_prefix -f -v 0.01 -m CV

Count2FPKM/TPM + Filtering (MAD method)

./RNAnorm -i count.input -o output_prefix -f -v 0.01 -m MAD