I have run Tophat fusion with paired-end RNA-Seq data, but was unsuccessful. The error says running 'long_spanning_reads' . then i split fastq file and run again. unfortunately it is showing same error.
could anyone help me in this process!!!
My command was -- tophat2 -o tophat_fusion -p 15 --fusion-search --keep-fasta-order --bowtie1 --no-coverage-search index_file unmapped1.fastq unmapped2.fastq