What is the procedure to install tophat

Question

[inayatmathe]

I have tried several attempts to install tophat but it is not working out. Any kind of help will be appreciated.

[swbarnes2]

https://twitter.com/lpachter/status/937055346987712512

"Please stop using TopHat"

from the author of TopHat.

[GenoMax]

Using conda (or mamba) is likely the easiest way. TopHat developers make a linux binary available. No installation should be needed for this.

Is there a specific reason you are trying to use TopHat. There are better/current RNAseq aligners like STAR that should be used instead. Using alignment-free methods like salmon requires significantly less resources and is fast to boot (does require that a transcriptome be available though).

[inayatmathe]

Thank you for your response, I wanted to align the ribo-seq reads to the reference genome. I know many of software packages are available some times it is confusing to choose the one on the basis of performance. I have already downloaded the tophat . I agree that it does not need any installation. But, at the same time it is probably necessary to have bowtie in the path to run the tophat.

May be I am not able to set the path of tophat along with bowtie. If you can please help me out in this regard.

Ans thank you for your recommendations, I will surely look into it

[GenoMax]

If you have proper version of bowtie2 installed then simply add it to your $PATH. export PATH=$PATH:/path_to/bowtie2 should take care of that problem.