Project

Create list of BAMs, both realigned WGS and RNA-Seq.

Sample information

Scripts here create dat/BPS.samples.dat and dat/BPS.expression.samples.dat, which contains the following columns for each sample used for processing related to the Structure and Expression plots, respectively.

• Barcode - any unique identifier
• disease - TCGA code of cancer type. Used only in TCGA_Virus workflow
• BAM_path - full path to BAM file realigned to human + virus reference
• REF_path - path to reference FASTA the BAM is aligned to. Expect to see index file by appending .fai to pathname.

TCGA_Virus workflow

Neither downloaded nor realigned BAMs are distributed with BreakPointSurveyor.

WGS Data

Analysis considers one sample only, a TCGA head and neck tumor sample with the barcode (TCGA-BA-4077-01B-01D-2268-08)

This sample has been realigned to a custom reference (see A_Reference for details.)

RNA-Seq Data

480+ RNA-Seq samples which serve as controls for calulating case relative expression are listed in BPS.expression.samples.dat. These data are required for stage L_Expression.

Note that large RNA-Seq datasets need not be downloaded. See M_RSEM_Expression for an example of expression analysis using TCGA preprocessed expression data.

Getting started

Edit and run 1_get_BAM_paths.sh to include information about sequence data used for creating structure plots.

If calculating RPKM data from RNA-Seq data, edit 2_make_RNASeq_paths.sh accordingly.