dekupl-computeNF

computeNF is a small utilitary that compute Normalization Factors (NF) from k-mer counts table. NF is the median of the ratios between sample counts and counts of a pseudo-reference obtained by taking the geometric mean of each k-mer across all samples.

Installation

Dependancies

• gcc compiler
• zlib

Installation from the sources

1. Clone the project: git clone https://github.com/Transipedia/dekupl-computeNF.git
2. Compile the software: make
3. Place computeNF binary somewhere accessible to your $PATH

Documentation

Usage:

computeNF counts.tsv[.gz]

computeNF expect only one argument: the k-mers counts table (possibly gzipped). This table is a TSV (Tabulated-Separated Value) file, with an header line containing the sample names, and onr k-mer by row with its associated counts for each sample.

Input example:

tag     sample1 sample2 sample3 sample4
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 627     357     345     446
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAC 2       6       9       10
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAG 16      15      25      28
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAT 11      10      11      10
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAGA 10      9       20      14
...

Output example

sample  normalization_factor
sample1 0.9831
sample2 1.2342
sample3 1.0023