Why Do I Get The Tophat Fusion Error: --Fusion-Search Not Recognized

Question

[KS]

Hey guys,

I am trying to find fusion junctions using tophat-fusion

I downloaded and installed tophat-fusion. But I am getting an error

tophat-fusion: option --fusion-search not recognized.

Here is the command I followed:

tophat -o tophat_MCF7 -p 8 --fusion-search --bowtie1 --no-coverage-search -r 0 /path/to/h_sapiens/bowtie_index SRR064286_1.fastq SRR064286_2.fastq

Did I do something wrong while installation process?

Any kind of help is greatly appreciated

Thanks

Suz

Answer 1

[Istvan Albert]

Make sure to install the version of tophat that does include the --fusion-search option. Only the latest versions do.

TopHat2 is released in which TopHat-Fusion is included (04/09/2012)

[User 59]

Indeed tophat-fusion does not have a ---fusion-search option. Tophat2 does (and can be run with bowtie1 or bowtie 2 underlying the fusion search)