Inquiries about TeloExplorer and CentroMiner
OZTaekOppa opened this issue · comments
Hi,
Thank you for the excellent program.
Before proceeding further, I have a few questions regarding TeloExplorer and CentroMiner.
TeloExplorer: According to the manual, it offers three options: -c (plant, animal, other). I assume "animal" would be suitable for humans. However, what about aquatic species like fish, bivalves, and crustaceans? Would the "other" option be appropriate for aquatic species?
CentroMiner: The manual doesn't specify considerations for different phyla. Is this analysis solely based on the TE annotation file, regardless of species or phylum? If yes, this pipeline should be applicable to aquatic species, provided the proper TE annotation file is provided. Is my understanding correct?
Any feedback would be greatly appreciated.
- "animal" will use a highly conserved telomere repeat TTAGGG, including fishes. For bivalves and crustaceans I'm not very sure. However, setting "other" will use TIDK to identify the possible telomere repeat, so it normally results in the same.
- CentroMiner search candidates mainly based on tandem repeat. It works better on the species that tandem repeat is enriched in the centromere region. If not, you may need to further check the other non-best candidates.
Thank you for your insights.
I will get back to you after testing a few datasets.
Does the TEcoverage and the TElength in the centro output includes all TE and does it includes TR how did you calculate it ?
Include all kinds of LTR, as they are marked as LTR. It doesn't include TR. Calculated from input TE annotation.
Meanwhile, these two fleid has been removed in new version. TE still indicate LTR, sorry.