Please report "XXX not found in the TE_SO database" here!

[oushujun]

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!