JBerthelier
TEs classified as potential chimeric
Hello Jeremy is it a wise choice to include TEs classified as potential chimeric in your TE library. If not what if an Order includes TEs classified as only potential chimeric. For example, in my study Crypton have only two TEs classified as potential chimeric
Dear Lukanyo,
The problem with chimeric TEs is that they can be false positive TE sequences.
Then, if you want to be sure that they are true TE sequences, you must manually check them (
For example check their protein domain, example LTR --> reverse transcriptase
Crypton are very rare TE Order, you must check if this Order is know to be present in the Group of organisms you are studying.
If only two sequences have been found, they are probably false positives.
However, you can manually check these detected sequences and see if they have known motifs /protein domain found in Crypton etc ...
Best,
Jeremy
Alright thank you so much, much apreciated. Also, I can see in your study you further sort the classified sequences at the superfamily level based on evidence section of PASTEC. What if now some of other TE sequences of an order e.g TIR are not classified at superfamily level? wheres others are classified at superfamily level. Thats the challenge I have, hence i decided to only sort the classified sequences at order level, and build FASTA file of each TE orders, suject the FASTA files of respective orders to MCL
Dear Lukanyo,
When some TEs are only classified at Order you can keep them and just specify TIR/unclassified, instead of TIR/Mariner (for example).
Best,
Jeremy