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aaranyue / quarTeT

A telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification
http://atcgn.com:8080/quarTeT/home.html
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Inquiries about TeloExplorer and CentroMiner #30

Closed OZTaekOppa closed 2 months ago

OZTaekOppa commented 6 months ago

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.

Echoring commented 6 months ago
  1. "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.
  2. 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.
OZTaekOppa commented 6 months ago

Thank you for your insights. I will get back to you after testing a few datasets.

Isoris commented 4 months ago

Does the TEcoverage and the TElength in the centro output includes all TE and does it includes TR how did you calculate it ?

Echoring commented 3 months ago

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.