[Bioc-devel] Experimental data package 'seqc'

Wei Shi shi at wehi.EDU.AU
Tue Nov 18 23:52:03 CET 2014

We have created a new experimental data package called 'seqc'. It includes gene-level read count data generated by the SEQC (SEquencing Quality Control) project, which is the third stage of the well-known MAQC project (a US FDA initiative). The SEQC/MAQC-III Consortium produced benchmark RNA-seq data for the assessment of RNA sequencing technologies and data analysis methods (published recently on Nature Biotechnology - http://www.ncbi.nlm.nih.gov/pubmed/25150838):

Sequence reads were aligned to human reference genome hg19 using the Subread aligner and were then summarized to genes using the featureCounts program. This package includes the gene-level read count data for 2,758 libraries. It can be downloaded from the following link (188MB):


In addition to the read count data, this package also includes exon-exon junction data generated for human brain reference RNA and universal human reference RNA samples. Exon-exon junctions were detected by using the Subjunc aligner.

Moreover, TaqMan RT-PCR validation data for ~1000 genes and ERCC spike-in sequence data are included in this package as well.

We hope this package is a useful resource for the community.


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