meta data for this page
  •  

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revisionPrevious revision
Next revision		Previous revision
general:computerenvironment:software:trinity [2024/04/24 07:05] – freyageneral:computerenvironment:software:trinity [2024/04/24 09:37] (current) – [Running Trinity] freya
Line 11: Line 11:
 **Example code:** **Example code:**
 <code> <code>
-Trinity --seqType fq --max_memory 64G --left Path/to/forward/reads.fq \ +Trinity --seqType fq --max_memory 64G --left <Path/to/forward/reads.fq> \ 
---right Path/to/reversed/reads.fq --output path/to/output/location/ --verbose --CPU 12 --no_normalize_reads+--right <Path/to/reversed/reads.fq> --output <path/to/output/location/>Trinity/ --verbose --CPU 12 --no_normalize_reads
 </code> </code>
  
-Think about which of the parameters are important and why - maybe you can leave some of them out. For more options visit the [[https://github.com/trinityrnaseq/trinityrnaseq/wiki/Running-Trinity#running-trinity|Trinity site]] or open the %%--%%help in the terminal. It also should be mentioned that when running the script over the slurm controller, the memory and CPU count should be equal to the amount stated in the script.+Think about which of the parameters are important and why - maybe you can leave some of them out. Also check your version of Trinity - if options are not available that indicates that you have not installed the latest version (ask your tutor for help). For more options visit the [[https://github.com/trinityrnaseq/trinityrnaseq/wiki/Running-Trinity#running-trinity|Trinity site]] or open the %%--%%help in the terminal. It also should be mentioned that when running the script over the slurm controller, the memory and CPU count should be equal to the amount stated in the script.
  
 ===== Output ===== ===== Output =====