After I executed Trinity, I obtained 2 files as assembly transcripts.fasta and log.txt files.
I would like to know that is it possible to download ‘Trinity.fasta.gene_trans_map’ from Galaxy Trinity. It is important for my downstream analysis.
Thank you so much,
Hi, This report is not currently output from Trinity as wrapped for Galaxy at https://usegalaxy.org, but you can parse out the information from the fasta results.
Try this workflow: Galaxy
There are many ways to manipulate data. The tools I included in the workflow are simplified, and just one example of how to do this.
Trinity wiki that describes the fasta title line formatting: Output of Trinity Assembly · trinityrnaseq/trinityrnaseq Wiki · GitHub
Sample of a ‘Trinity.fasta.gene_trans_map’ file: https://github.com/trinityrnaseq/trinity_ext_sample_data/blob/master/test_DATA/Trinity.fasta.gene_trans_map
The latest version of the
Trinity tool, by default, now includes an additional output dataset named “Gene to transcripts map”. Any version of
Trinity at this revision or higher will produce the same additional output:
Trinity de novo assembly of RNA-Seq data (Galaxy Version 2.9.1)
The overall update of the
Trinity tool suite also includes several other wrapped components. For the full list, please see the Main ToolShed repository: https://toolshed.g2.bx.psu.edu/view/iuc/suite_trinity/4a453a8da3b5.
Public Galaxy servers that have chosen to host the tool suite will generally place these tools under the RNA-seq tool panel group. Or, you can use the tool search to locate tools quickly.
The prior version of
Trinity is considered deprecated now. At Galaxy Main https://usegalaxy.org, the final stages for that are still in progress. Once done, this ticket will close out: https://github.com/galaxyproject/usegalaxy-playbook/issues/143
In short, all end-users should 1) use the updated tool versions if at all possible and 2) be careful not to use the output from the older tool as an input to the updated tools.
If the older output is really needed for some reason, be sure to carefully review downstream tool forms and make adjustments to your data as needed. Many accept a variety of custom assembly outputs, and for some tools, the prior
Trinity results should be considered to be a “custom format” due to changes in key data attributes (such as fasta title lines) between the two tool versions.