Entering edit mode
3.0 years ago
inayatmathe
•
0
I have tried several attempts to install tophat but it is not working out. Any kind of help will be appreciated.
I have tried several attempts to install tophat but it is not working out. Any kind of help will be appreciated.
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https://twitter.com/lpachter/status/937055346987712512
"Please stop using TopHat"
from the author of TopHat.
Using
conda
(ormamba
) 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 likeSTAR
that should be used instead. Using alignment-free methods likesalmon
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.