Re. De Novo Assembly for RNA seq Data using Trinity

[Hamad]

Hi Everyone,

I am trying to run De Novo Assembly for (Schizosaccharomyces pombe) and follow the steps described by (Haas., et al paper). In the methods section, they used Trinity software in order to do the De Novo Assembly and I'm just trying to reproduce what they did in the paper.

I'm using the school server which has Trinity to do this but I wasn't able to unpack the file that has the RNA fq sequences reads when I used this command:
tar –xvf TrinityNatureProtocolTutorial.tgz

Also using Terminal linux commands in my Mac, how can I add RNA seq data to a new directory and view the right and left fq reads to be able to Run Trinity.

Sorry, I am new to this.

Thank you so much in advance.

[jfo]

Hi Hamad,

to uncompress tgz files you should use:

tar –xzvf TrinityNatureProtocolTutorial.tgz -C new_dir

-z to use gnuzip
-C to specify the directory where the extracted files will be placed

Good luck!