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 [2023/04/24 09:13] – [Running Trinity] freyageneral:computerenvironment:software:trinity [2024/04/24 09:37] (current) – [Running Trinity] freya
Line 3: Line 3:
 Trinity is a de Bruijn graph based //de novo// assembler for RNA seq data. It has been published in 2011 by {{mbw_bioinf:wiki:mbw:literature:grabherr2011.naturebiotech.pdf|Grabherr et al. in Nature Biotechnology}}. As with all our software tools, Trinity is not necessarily the all time best solution for assembling RNA seq data, however, it is certainly a good start. You can find a presentation of how to run Trinity assemblies {{mbw_bioinf:wiki:mbw:slides:trinity_workshop_part1-1.pdf|HERE}}. Trinity is a de Bruijn graph based //de novo// assembler for RNA seq data. It has been published in 2011 by {{mbw_bioinf:wiki:mbw:literature:grabherr2011.naturebiotech.pdf|Grabherr et al. in Nature Biotechnology}}. As with all our software tools, Trinity is not necessarily the all time best solution for assembling RNA seq data, however, it is certainly a good start. You can find a presentation of how to run Trinity assemblies {{mbw_bioinf:wiki:mbw:slides:trinity_workshop_part1-1.pdf|HERE}}.
  
-Haas et al. 2013 published a protocol that describes the use of Trinity in the reconstruction of transcripts using a de novo assembly strategey. Follow this {{mbw_bioinf:wiki:mbw:literature:haas2013.naturebiotech.pdf|LINK}}  to access the publication. +Haas et al. 2013 published a protocol that describes the use of Trinity in the reconstruction of transcripts using a de novo assembly strategey. Follow this {{mbw_bioinf:wiki:mbw:literature:haas2013.naturebiotech.pdf|LINK}} to access the publication.
- +
-=====   =====+
  
 ===== Running Trinity ===== ===== Running Trinity =====
Line 13: Line 11:
 **Example code:** **Example code:**
 <code> <code>
-perl /Path/to/Trininty/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+Trinity --seqType fq --max_memory 64G --left <Path/to/forward/reads.fq> \ 
 +--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 =====