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gene_trans_maps/Fracy.gene_trans_map -transcript_fasta. However, when I run the 'Trinotate trinotate.sqlite init' command, I get the following output and error:ĬMD: /scratch/mparks/bin/Trinotate-3.0.2/util/trinotateSeqLoader/ -sqlite trinotate.sqlite -gene_trans_map.

As one example, I have the following gene_trans_map formatting which I believe is essentially identical to Matt Krosch's:įracy1_FilteredModels1.jgi|Fracy1|144970 Fracy1_FilteredModels1.jgi|Fracy1|144970|gw1.31.119.1įracy1_FilteredModels1.jgi|Fracy1|250403 Fracy1_FilteredModels1.jgi|Fracy1|250403|fgenesh2_pg.31_#_2įracy1_FilteredModels1.jgi|Fracy1|197108 Fracy1_FilteredModels1.jgi|Fracy1|197108|e_gw1.31.238.1 I am also trying to run Trinotate on several non-Trinity transcriptomes, in this case downloaded from both GenBank and JGI. Not sure if this thread is still active, but I have a question related to Matt Krosch's post above. Any idea on why this could be happening? Any input would be greatly appreciated So basically it seems to be ignoring completely the information on my provided map file. However when running the align and estimate abundance script with the -gene_trans_map option, my RSEM outputs look like this:

To me more accurate, the data were assembled with trinity and afterwards i used Corset to cluster them.

I came across this post while trying to find a solution to a similar problem I am having, when trying to run the scripts within trinity on a non-trinity assembly.