LncRNA-ID

This project contains supporting scripts and data for the paper Long non-coding RNA IDentification using balanced random forest by Rujira Achawanantakun, Yanni Sun, and Yuan Zhang.

Files

Scripts:

expression.sh: calculate expression in coding region and 3'utr

getSeqFromGenome.sh: get genes and lncRNAs from genomic sequence

getSequenceFromBedFile.sh: get sequences from Bed format files

DNA2Protein.cpp: Tranlsate DNA sequences into a protein sequence using multiple frame translations

Data:

The data are available for download at here.

The data files used in our experiments are organized into the following four folders:

1. H1_gencode/ : the human GENCODE data set (H1)

2. M1_gencode/ : the mouse GENCODE data set (M1)

3. H2_cpat/ : CPAT’s human data set (H2)

4. M2_ribosomeRelease/ : experimentally verified mouse lncRNA data set (M2)