Looking For Reasons Of Why The Results Of A Tophat Fusion Post Is Empty

Question

[KS]

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

[samsara]

have you checked the log files? I did not put human blast databases inside folder blasthuman. I extracted all archives under blast directory.

Answer 1

[nicolas.robine]

I think I found the problem (after many errors). On line 696 of the script tophat-fusion-post, I saw:

        if string.find(file, "tophat_") != 0:

And I rename the folders tophat_ (in the above case tophat_MCF7), it seems to work! I hope that can be useful to others!

[Mikael Huss]

Thanks, finally a ray of hope :-)

Answer 2

[Mikael Huss]

You're not the only one! See these SeqAnswers threads, maybe they can provide some help:

Repost: tophat-fusion outputs empty result

tophat-fusion-post result empty

I have been unable to solve the problem in my own case, and instead moved on to other fusion finding programs like FusionCatcher, ChimeraScan, FusionMap, and FusionHunter (which I have all managed to run, although not without some trial-and-error).

Answer 3

[Paul]

I have got it - mcl (known gene fusions) can be obtained from previous tophatfusion version (in annotation directory), http://tophat-fusion.sourceforge.net/downloads/tophatfusion-0.1.0.tar.gz