The TRate program computes "rate" of each transcript according to given coverage file. Transcripts are coded by coordinates of their exons (bed file for now, gtf/gff in future). Rate is computed as total mass of exons within the transcript divided by total length of exons. Mass is taken as approximation of the area under coverage curve, i.e. sum of areas of coverage rectangles, and length is computed as sum of lengths of bedgraph intervals within exons.
The TRate program takes in two arguments in fixed order.
- Exons_file - coordinate sorted bed file that provides locations of exons for the corresponding transcript provided in column 4.
Exons_file format example
C0000570 10420 10640 Transcript1
C0000570 128078 128167 Transcript2
C0000570 128290 128405 Transcript2
C0000571 72845 73133 Transcript3
C0000571 73211 73274 Transcript3
- Coverage_file - coordinate sorted file in bedgraph format - it can contain coverage data (usually normalized) from RNAseq study, ChIPseq, ATACseq and so on.
Coverage_file format example
C0000570 10481 10549 0.310587
C0000570 10579 10610 0.41057
C0000570 128288 128293 1.105
BEDTOOLS
AWK
g++
Download TRate
cd TRate
make
In file TRate.sh edit path to TRate folder, e.g.
FOLDER_PATH="your/path/TRate"
./TRate.sh ./data/Exons_file.sbed ./data/Coverage_file.bg
Output will be in a file Coverage_file.rate.
Output format
Transcript1 0.341895
Transcript2 1.98961
Transcript3 -1
Transcript rate = -1 if no coverage data were found for this transcript.