We used STAR v2.6.1d to align paired-end RNA-seq reads. This output was used for all subsequent RNA analysis. The reference we used was that of ENSEMBL's GENCODE 27, "Comprehensive gene annotation." We used RSEM v1.3.1 for transcript- and gene-level quantification. We also added a second method of quantification using Kallisto v0.43.1. This method differs in that it uses pseudoaligments using fastq reads directly to the aforementioned GENCODE 27 reference.
We set up Arriba v1.1.0 and STAR-Fusion 1.5.0 fusion detection tools using CWL on CAVATICA.
For both these tools we used aligned BAM and chimeric SAM files from STAR as inputs and GRCh38_gencode_v27 GTF for gene annotation.
We ran STAR-Fusion with default parameters and annotated all fusion calls with GRCh38_v27_CTAT_lib_Feb092018.plug-n-play.tar.gz provided in the STAR-fusion release.
For Arriba, we used a blacklist file blacklist_hg38_GRCh38_2018-11-04.tsv.gz from the Arriba release tarballs to remove recurrent fusion artifacts and transcripts present in healthy tissue.