Computational protocol: An Efficient Method for Identifying Gene Fusions by Targeted RNA Sequencing from Fresh Frozen and FFPE Samples

Similar protocols

Protocol publication

[…] Resulting sequences were analyzed in the following ways: 1. To determine the reads that were derived from targeted RNA sequences, forward reads were mapped to the Hg19 reference genome using STAR v2.4.0d [] only allowing unique alignment and allowing chimeric reads. Bedtools intersect [] was then used to count the number of sequenced reads that were derived from targeted transcripts using default settings, and 2. paired-end sequence data were analyzed for the presence of gene fusions with SOAPFuse v1.22 software [] with default settings.For publically available UHR RNA-Seq data, we downloaded SRX333353 [] and for HCC1937 we downloaded SRX317716 []. […]

Pipeline specifications

Software tools STAR, BEDTools, SOAPfuse
Application RNA-seq analysis
Diseases Neoplasms
Chemicals Formaldehyde