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Old 08-15-2018, 08:03 PM   #1
Junior Member
Location: Austin

Join Date: Jul 2018
Posts: 1
Smile Re. De Novo Assembly for RNA seq Data using Trinity

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.
Hamad is offline   Reply With Quote
Old 10-31-2018, 08:39 AM   #2
Junior Member
Location: SE Asia

Join Date: Oct 2016
Posts: 4

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!
jfo is offline   Reply With Quote

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