Well, TE classifications are MESSY! All sort of naming conventions and alias are floating around.
I created the TE_Sequence_Ontology.txt file in EDTA/bin/ to collect all these names, and use the Sequence Ontology system to serve as a standardized naming system. I have been collecting these names FOR YEARS, BUT still, I still encounter new ones!
So, if you see warnings messages like the ones below, please copy the unique warning lines and paste them here.
PLE/Chlamys not found in the TE_SO database, it will not be used to rename sequences in the final annotation.
Warning: DNA/MarinerTc1 not found in the TE_SO database, will use the generic term 'repeat_fragment SO:0001050' to replace it.
Please try not to paste the whole report...
Here's a line that can help to grep the problematic names, please paste the result in this thread:
cat YOUR_EDTA_REPORT.txt | grep TE_SO | sed 's/Warning: //' | awk '{print $1}' | sort | uniq -c | sort -k1,1 -rn
Thank you for contributing!
Well, TE classifications are MESSY! All sort of naming conventions and alias are floating around.
I created the TE_Sequence_Ontology.txt file in EDTA/bin/ to collect all these names, and use the Sequence Ontology system to serve as a standardized naming system. I have been collecting these names FOR YEARS, BUT still, I still encounter new ones!
So, if you see warnings messages like the ones below, please copy the unique warning lines and paste them here.
PLE/Chlamys not found in the TE_SO database, it will not be used to rename sequences in the final annotation.Warning: DNA/MarinerTc1 not found in the TE_SO database, will use the generic term 'repeat_fragment SO:0001050' to replace it.Please try not to paste the whole report...
Here's a line that can help to grep the problematic names, please paste the result in this thread:
cat YOUR_EDTA_REPORT.txt | grep TE_SO | sed 's/Warning: //' | awk '{print $1}' | sort | uniq -c | sort -k1,1 -rnThank you for contributing!