This code was developed by Roberto Vera Alvarez (r78v10a07@gmail.com) and Leonardo Mariño-Ramírez (l.marino.ramirez@gmail.com) to calculate the TPM values for introns and exons from a SAM files and a GTF file.

The program was tested using genes.gtf file from hg19 (UCSC).

Papers used:

1. Wagner GP, Kin K, Lynch VJ. Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples. Theory Biosci. 2012 Dec;131(4):281-5. doi: 10.1007/s12064-012-0162-3. https://www.ncbi.nlm.nih.gov/pubmed/22872506

2. The SAM/BAM Format Specication Working Group. Sequence Alignment/Map Format Specication. http://samtools.github.io/hts-specs/SAMv1.pdf

Install:

For GNU/Linux and MAC OSX with Makefile installed.

Type make for compilation and make test for testing the library

Files:

gTools/dist/Release/libgtools.a
TPMCalculator/dist/Release/TPMCalculator
TPMOutPutMerger/dist/Release/TPMOutPutMerger