Thread: Tuxedo suit
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Old 06-01-2017, 01:00 PM   #1
Nathan Seth
Junior Member
Location: South Africa

Join Date: Jun 2017
Posts: 1
Default Tuxedo suit


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.
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