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:
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