Hello Everyone,

I ran tophat-2.7 on the example data with --fusion-search , it ran successfully and produced the following output files: accepted hits.bam, deletions.bed, insertions.bed, junctions.bed, fusions.out

I am trying to run tophat-fusion-post, after I run it, the output is empty. Can anyone suggest the reason for it?

The command I used to run tophat (I am retuning this command under topdir directory):

tophat -o tophatMCF7 -p 8 --fusion-search /path/to/hsapiens/bowtieindex/hg19 SRR0642861.fastq SRR0642862.fastq

The structure I am using to run tophat is the following:

top_dir:

blast
blasthuman (nt and humangenomic databases)
indexes (hg19)
mcl
refGene.txt
ensGene.txt
SRR0642861.fastq 
SRR0642862.fastq
tophatMCF7 (output directory): accepted_hits.bam, deletions.bed, insertions.bed, junctions.bed, fusions.out, logs, prep_reads.info, unmapped.bam