Is it possible to download 'Trinity.fasta.gene_trans_map' from Galaxy Trinity?

trinity

#1

Dear all,

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,
Kamoltip


#2

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: https://usegalaxy.org/u/jen/w/create-trinityfastagenetransmap

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.

References

Trinity wiki that describes the fasta title line formatting: https://github.com/trinityrnaseq/trinityrnaseq/wiki/Output-of-Trinity-Assembly

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

Thanks!