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Old 02-13-2013, 11:00 AM   #1
suz.katie
Junior Member
 
Location: Virginia

Join Date: Dec 2012
Posts: 2
Default Tophat-fusion error

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
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Old 02-13-2013, 01:23 PM   #2
Bukowski
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Location: UK

Join Date: Jan 2010
Posts: 390
Default

tophat2 has the --fusion-search option - tophat1 one does not.

tophat-fusion is based on tophat1 and is a separate piece of software. Tophat2 includes it as standard.

You can run --fusion-search in tophat2 with either bowtie1 or bowtie2 as the underlying mapper.
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