bash: tophat: command not found

Question

[gmangse01]

Dear all,

I'm new to both RNAseq and this group. I installed the 'old tuxedo site' on my Mac computer following instructions in the 'Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks' paper. I've tried to run the first command as follows: 'tophat -p 8 -G genes.gtf -o C1_R1_thout genome.fa GSM794483_C1_R1_1.fq GSM794483_C1_R1_2.fq'. Each time it returns with the message 'bash: tophat: command not found'. I'm not sure what i've done wrong.

Can someone help please?

Thanks,

George.

[Jon]

I know not part of your question, but TopHat is deprecated and even the developers have told people to stop using it. Their replacement aligner is called hisat2.

[GenoMax]

Second this.
gmangse01 : if you need directions for HISAT like the ones you have for TopHat then follow this Nature Protocols paper.

[GenoMax]

See this to fix the problem above.

Spend some time here getting familiar with basic unix. Best investment you will make.

[cpad0112]

Download mac os x binary from http://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.OSX_x86_64.tar.gz and keep it in your path. To know the path, type echo $PATH in your bash shell. Keep tophat binary in one of these paths. Or keep it in a directory and add that directory to user (your) shell path.

Answer 1

[colindaven]

Why not have a look at a modern pipeline such as NGI-RNA-seq https://github.com/SciLifeLab/NGI-RNAseq ? This will get you going a lot quicker. Also, I'd recommend using Linux over Mac since most software is better supported there.

[WouterDeCoster]

Also, I'd recommend using Linux over Mac since most software is better supported there.

I don't use Mac but I don't think this is true.