pcawg3-alternative-promoter

This pipeline is developed as part of PCAWG project to estimate promoter activity from RNA-Seq data using transcript expression estimates. The promoter and gene centric tables can be created for alternative promoter phenotype using this pipeline.

Required files

The following 3 files are required to run the alternative promoter analysis:

1. PCAWG Metadata file: This file has been published as part of the PCAWG data and can be obtained from: https://dcc.icgc.org/api/v1/download?fn=/PCAWG/transcriptome/metadata/rnaseq.extended.metadata.aliquot_id.V4.tsv.gz
2. PCAWG Transcript expression table file: This file has been published as part of the PCAWG data and can be obtained from: https://dcc.icgc.org/api/v1/download?fn=/PCAWG/transcriptome/transcript_expression/pcawg.rnaseq.transcript.expr.fpkm.tsv.gz
3. Gencode v19 txdb file: We created a txdb object using the GTF file for Gencode v19 (https://www.gencodegenes.org/human/release_19.html). The txdb file can be downloaded from: https://drive.google.com/open?id=1Uhp65KqCPupRUWwrPgyxTCFuSO5Yul2d

How to run

The main file can be found at "./R/geneCentricAnalysis-promoter.R". The user needs to change the paths for the input files. The script will calculate the promoter activities, coordinates, promoter and gene centric tables.

Citing this pipeline

If you use this pipeline, please cite: Calabrese, C., Davidson, N.R., Fonseca, N.A., He, Y., Kahles, A., Lehmann, K.-V., Liu, F., Shiraishi, Y., Soulette, C.M., Urban, L., et al. (2018). "Genomic basis for RNA alterations revealed by whole-genome analyses of 27 cancer types" bioRxiv, 183889.

Contributors

This pipeline is developed and maintained by Deniz Demircioglu and Jonathan Göke.