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r78v10a07 authored Dec 5, 2018
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21 changes: 2 additions & 19 deletions README.md
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Expand Up @@ -92,25 +92,8 @@ used for TPM calculation.

## Validation

To validate our software, we calculate the Pearson correlation coefficient between TPM and FPKM
for normalized expression values using RNA-Seq data of 1,256 samples from
the TCGA-BRCA project.

![Correlation Plot](https://github.com/ncbi/TPMCalculator/raw/master/doc/TPMCalculator_RSeQC.png)

Additionally, the correlation coefficient was also calculated for the raw read counts
reported by TPMCalculator, HTSeq and featureCounts.

<img src="https://github.com/ncbi/TPMCalculator/raw/master/doc/TPMCalculator_HTSEq.png" alt="Correlation Plot" width="888" />
<img src="https://github.com/ncbi/TPMCalculator/raw/master/doc/TPMCalculator_featureCounts.png" alt="Correlation Plot" width="888" />

### Table S3: Correlation coefficient between TPMCalculator and the three tools for the samples with low correlation at least for one tool. Color scale: green high correlation and white low correlation

<img src="https://github.com/ncbi/TPMCalculator/raw/master/doc/TableS3.png" alt="Correlation Plot" width="888" />

TPMCalculator reduces the compute time and the resource requirements of RNA-Seq pipelines
by eliminating multiple steps. For example, TPMCalculator processes BAM files of size 7.0 GB
in ~20 minutes requiring only 4GB of RAM.
* [UCSC hg19](https://github.com/ncbi/TPMCalculator/wiki/Validation#validation-using-ucsc-hg19-genome-annotation)
* [Gencode v25](https://github.com/ncbi/TPMCalculator/wiki/Validation#validation-using-gencode-v25-genome-annotation)

For more detailed description and instalation guide lines see https://github.com/ncbi/TPMCalculator/wiki/

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