FusionSeq Test Datasets

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Two datasets are available to test FusionSeq: NCIH660 and GM12878 cell-line data. These datasets are part of FusionSeq dataset, published in Genome Biology, 2010;11:R104. Please note that the full set, including cancer samples, will be available at dbGaP soon, where confidentiality issues are taken care of properly. We here provide the cell-line data in different formats:

Mapped Read Format (MRF)

This is the format required by FusionSeq. RSEQtools provide several conversion tools to generate MRF files from the most popular alignment tools.

• GM12878.mrf.gz
• NCIH660.mrf.gz

Please read 'How to execute FusionSeq' section for more detail on how to use these files.

FASTQ

FASTQ is a text-based format for storing both a biological sequence and its corresponding quality scores. Each tarball includes two FASTQ files, one for each end.

• GM12878.fastq.tar.gz
• NCIH660.fastq.tar.gz

BAM

BAM format is the binary compressed format of SAM (Sequence Alignment/Map). We provide both BAM files and their corresponding index files (*.bai) so that they can be viewed with the Integrative Genome Viewer (IGV) a high-performance visualization tool for interactive exploration of large, integrated datasets from the Broad Institute.

• http://rnaseq.gersteinlab.org/fusionseq/datasets/GM12878.bam
• http://rnaseq.gersteinlab.org/fusionseq/datasets/GM12878.bam.bai
• http://rnaseq.gersteinlab.org/fusionseq/datasets/NCIH660.bam
• http://rnaseq.gersteinlab.org/fusionseq/datasets/NCIH660.bam.bai

You can download the files locally or load them into IGV directly. See instructions at http://www.broadinstitute.org/igv/.