I used STAR to analyze the paired-end reads and then STAR-fusion with the chimeric junctions file from STAR to detect fusion transcripts. The K562 SRA file from NCBI is used for the test run. The reference genome, GTF file and BLAST+ result file are all obtained from CTAT-RESOURCE-LIB. The galaxy run page is set up as shown in snapshot below. Although the chimeric junctions file from STAR shows 1.4M hits, no fusion transcript was detected by the STAR + STAR fusion. The output showed zero line.
I noticed that the version of STAR fusion 0.54 is really out of date and is probably incompatible with the STAR version 2.78a in galaxy. I actually tried different versions of STAR, but got the same results with zero lines in the outputs.
I believe this is the compatibility issue with STAR fusion. Is it possible for galaxy developers to update the STAR fusion version in galaxy?
