search

hyunhwan-jeong / SalmonTE

SalmonTE is an ultra-Fast and Scalable Quantification Pipeline of Transpose Element (TE) Abundances
GNU General Public License v3.0
81 stars 23 forks source link

"Non-supported" species #64

Closed amitjavilaventura closed 2 years ago

amitjavilaventura commented 2 years ago

Dear Hyun-Hwan Jeong,

I want to try salmonTE with species that are not in the supported ones (according to the documentation: mm, hg, dr and dm).

I was wondering whether I can build indexes for these species and use those for subsequent analyses. They are not present in RepBase, but I can download the repeat masker sequences (all TEs) from the UCSC.

Is it possible to do this?

Thank you in advance.

Best regards, Adrià.

hyunhwan-jeong commented 2 years ago

Sorry for the late response, @amitjavilaventura. I wonder you have finished creating the reference file - if you don't please describe that what species you want to try to build a reference.

Thank you,

Hyun-Hwan Jeong