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Old 06-01-2017, 01:00 PM   #1
Nathan Seth
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Location: South Africa

Join Date: Jun 2017
Posts: 1
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I am rying to run tophat it doesnt seem to work.
i have loaded the modules and everything(i think) nothing!
i think its something wrong with my script!
Please help

bowtie2-build Arabidopsis_thaliana.fa Arabidopsis_thaliana

tophat2 p 5 -library-type fr-firststrand -o Control1_tophat_output Arabidopsis_thaliana Control1_trimmed.fq
tophat2 p 5 -library-type fr-firststrand -o Control2_tophat_output Arabidopsis_thaliana Control2_trimmed.fq
tophat2 p 5 -library-type fr-firststrand -o Control3_tophat_output Arabidopsis_thaliana Control3_trimmed.fq
tophat2 p 5 -library-type fr-firststrand -o Case1_tophat_output Arabidopsis_thaliana Case1_trimmed.fq
tophat2 p 5 -library-type fr-firststrand -o Case2_tophat_output Arabidopsis_thaliana Case2_trimmed.fq
tophat2 p 5 -library-type fr-firststrand -o Case3_tophat_output Arabidopsis_thaliana Case3_trimmed.fq

Last edited by Nathan Seth; 06-01-2017 at 02:01 PM.
Nathan Seth is offline   Reply With Quote
Old 06-01-2017, 07:38 PM   #2
Location: MA, USA

Join Date: Feb 2014
Posts: 58

Maybe try "-p 5" instead of "p 5"?
neavemj is offline   Reply With Quote
Old 06-02-2017, 01:20 AM   #3
Location: Antwerp, Belgium

Join Date: Oct 2015
Posts: 97

That's probably it. Also, it's very helpful to show the error message you get.
wdecoster is offline   Reply With Quote
Old 06-02-2017, 03:58 AM   #4
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,101

In addition to previous suggestions, some options require two hyphens (e.g. --library-type fr-firststrand).
GenoMax is offline   Reply With Quote

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