search

CSU-KangHu / HiTE

High-precision TE Annotator
GNU General Public License v3.0
46 stars 1 forks source link

TE classification issue #18

Open ZhenyanLuo opened 2 weeks ago

ZhenyanLuo commented 2 weeks ago

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 commented 2 weeks ago

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