I have tried several attempts to install tophat but it is not working out. Any kind of help will be appreciated.
"Please stop using TopHat"
from the author of TopHat.
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).
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
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.
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