Tuxedo suit

[Nathan Seth]

Hello!

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

[neavemj]

Maybe try "-p 5" instead of "p 5"?

[wdecoster]

That's probably it. Also, it's very helpful to show the error message you get.

[GenoMax]

In addition to previous suggestions, some options require two hyphens (e.g. --library-type fr-firststrand).