TE classification issue

[ZhenyanLuo]

Hi,

I found several TE families which were classified as TIR in early stages, but then classified as Gypsy in the final output: HiTE.out (see below). I have manually checked motifs in consensus sequences of these TE families and can confirm they are actually Gypsy. I was wondering whether I should trust the column 11 in all the cases like this?

9983 13.6 0.7 0.0 AU3_HapA_CHR01 26053 27651 (85564100) C TIR_374 Gypsy (0) 6448 4839 22
3719 25.2 0.1 1.8 AU3_HapA_CHR01 1676868 1677864 (83913887) C TIR_224 Gypsy (1850) 984 5 1532 *

Cheers,
Yan

[CSU-KangHu]

Hi @ZhenyanLuo,

Thank you for using HiTE. Based on your output, these sequences were identified by the TIR module but classified as Gypsy by the classifier, indicating some misclassifications. I recommend manually reviewing these sequences, as they may correspond to false positives or TE fragment sequences.

Best,
Kang