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hyunhwan-jeong / SalmonTE

SalmonTE is an ultra-Fast and Scalable Quantification Pipeline of Transpose Element (TE) Abundances
GNU General Public License v3.0
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coordinates of the TEs in clades.csv #63

Closed Xiaofei-git closed 2 years ago

Xiaofei-git commented 2 years ago

Hi @hyunhwan-jeong ,

How can I get the coordinates of the TEs in clades.csv. What is the reference version you used for mapping? I checked the salmonTE.py, but I did't find out.

The idea is to compare the expression of the TEs to the expression of neighboring genes, so I need to know the poison of TEs and the version of reference.

Thanks a lot!

hyunhwan-jeong commented 2 years ago

Hello @Xiaofei-git,

SalmonTE doesn't provide any locus information of TEs. You may think about using some database like RepeatMasker/dfam to find the locations. If you think it would be useful to include those types of information in SalmonTE, I would be welcome to hear your idea.

Kind regards,

Hyun-Hwan Jeong

Xiaofei-git commented 2 years ago

I will try to figure it out and let you know. Thanks for your reply!