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Old 06-21-2012, 01:36 AM   #1
MerFer
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Location: Germany

Join Date: Sep 2009
Posts: 21
Default Tophat2 fusion post

Dear Tophat2 user,

After I ran tophat2 with --bowti1 option I am now trying to run tophat-fusion-post.
My directory structure is
- top_dir
-tophat_sample_1
-tophat_sample_2
-ensGene.txt
-refGene.txt
-mcl
-blast (human_genomic* and nt*)
When I run post I get an error like
EXIT CODE 5
FATAL: Argument 1 ("-db") is not recognized or is improperly formed.

Do you have an idea what I am doing wrong?

thanks
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Old 06-26-2012, 09:46 AM   #2
NKAkers
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Default

Why don't you give the command that you tried to run. It sounds like you tried to use a -db option, which isn't supported by tophat-fusion-post.
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Old 06-29-2012, 03:37 AM   #3
MerFer
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Location: Germany

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the tophat fusion post from Tophat2 uses the newest version of blastn, which has a -db option instead of -d option. That's why I got the errors.

Thank you
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