Open Access Highly Accessed Methodology article

SERE: Single-parameter quality control and sample comparison for RNA-Seq

Stefan K Schulze, Rahul Kanwar, Meike Gölzenleuchter, Terry M Therneau* and Andreas S Beutler*

Author Affiliations

Departments of Oncology and Biostatistics, Mayo Clinic, Rochester, MN 55905, USA

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BMC Genomics 2012, 13:524  doi:10.1186/1471-2164-13-524

Published: 3 October 2012

Additional files

Additional file 1:

Contains the supplementary table and figures.

Format: PDF Size: 463KB Download file

This file can be viewed with: Adobe Acrobat Reader

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Additional file 2:

Is a table listing the exon boundaries for the rat annotation.

Format: ZIP Size: 2.3MB Download file

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Additional file 3:

Is a master read count table listing the number of reads for each exon in each of the 14 lanes.

Format: TXT Size: 12MB Download file

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Additional file 4:

Is an R script to create a hash index file by the ‘sample’ function in R that serves as input for Additional file 5.

Format: R Size: 2KB Download file

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Additional file 5:

Is the JAVA script to create the in silico replicates.

Format: JAVA Size: 8KB Download file

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Additional file 6:

Is the R code to calculate SERE.

Format: R Size: 1KB Download file

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Additional file 7:

Is an R script to calculate the confidence intervals for SERE.

Format: R Size: 1KB Download file

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Additional file 8:

Is the R code for the Kappa statistic on RPKM scale.

Format: R Size: 2KB Download file

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