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:
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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
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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