Tophat fusion error

Question

[baurumon]

Hi, 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

Answer 1

[Kevin Blighe]

You were working too late and your computer's battery was low, but this is not why the error occurred.

You may have run out of memory - difficult to know. There are many other programs to try if you cannot get TopHat-fusion working: A: Gene Fusion Detection: Rna-Seq Data

Kevin

[baurumon]

i am running it in cluster and there have plenty of free space . i did check the memory while using. Some sample data working well but other showing this issue. Thank you for other software recommendation but I am going through a specific pipeline.