This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to add path of cutadapt in trim_galore perl script?

Hi all. I want to use trim galore. I have installed both fastqc and cutadapt. When I run trimGalore, it gives me an error message stating that cutadapt is not installed although, I have installed it. I want to ask how to add the path of cutadapt in perl based trim_galore script to make it work?

next-gen
• 2,725 views • link
updated by padwalmk padwalmk • written by nadiabeg.comsats • nadiabeg.comsats

1 answer

Hi, Just check the first installation location of the cutadapt and fastqc by which command. If it's a nonstandard location then either you can export path by putting these lines to the .bashrc 

PATH=~/opt/bin:$PATH

replace /opt/bin with your path and put it in a ~/.bashrc

Another option is you can just copy cutadapt to the ~/local/bin or /usr/bin or /usr/local/bin, whatever you like.

• 0 views • link
updated by GenoMax GenoMax • written by padwalmk padwalmk

Thanks for your reply. I am still getting the same error. I am running my bash script on cluster may be cluster is an issue. Is there any alternative of trim-galore? What about Trimmomatic. Is it a good option?

• 0 views • link
written by nadiabeg.comsats • nadiabeg.comsats

I generally use, trimmomatic and its work perfect, just select trimming and window size according to the fastqc file.

• 0 views • link
written by padwalmk padwalmk

Log in to answer this question.

More posts like this