RNA-Seq: FusionHunter: identifying fusion transcripts in cancer using paired-end RNA-

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FusionHunter: identifying fusion transcripts in cancer using paired-end RNA-seq.

Bioinformatics. 2011 May 5;

Authors: Li Y, Chien J, Smith DI, Ma J

MOTIVATION: Fusion transcripts can be created as a result of genome rearrangement in cancer. Some of them play important roles in carcinogenesis, and can serve as diagnostic and therapeutic targets. With more and more cancer genomes being sequenced by next-generation sequencing technologies, we believe an efficient tool for reliably identifying fusion transcripts will be desirable for many groups. RESULTS: We designed and implemented an open-source software tool, called FusionHunter, which reliably identifies fusion transcripts from transcriptional analysis of paired-end RNA-seq. We show that FusionHunter can accurately detect fusions that were previously confirmed by RT-PCR in a publicly available dataset. The purpose of FusionHunter is to identify potential fusions with high sensitivity and specificity and to guide further functional validation in the laboratory. AVAILABILITY: http://bioen-compbio.bioen.illinois.edu/FusionHunter/ CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID: 21546395 [PubMed - as supplied by publisher]



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[Enrico Palazzo]

Hi,

your sample data bases on hg18 and its' annotations. Could you please describe how to prepare hg19 annotation files properly? Or: much better Could you provide these files as a download?

And another question: Is there a lower limit in read length? I'm trying to run FusionHunter on 2*36bp reads. Thus, I have to set the segment size to 18bp (as you suggested in FusionHunter.cfg). Could this be too short?

Thanks in advance!