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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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to build indices #53

Closed amitpande74 closed 2 years ago

amitpande74 commented 3 years ago

HI, Can you kindly explain this command SalmonTE.py index [--ref_name=ref_name] (--input_fasta=fa_file) [--te_only] I know that the input fasta should be the hg19 but for --te_only which format should be used ? GTF or the BED.

regards.

hyunhwan-jeong commented 3 years ago

@amitpande74,

First, I think this question is related #50, and I have attached my answer:

Dear Yong,

SalmonTE doesn't requires any GTF file to build an index, and it only requires fasta file. I am not sure how you tried to build your index. If you want to have a support from me, you probably need to share details of your data.

Thank you,

Hyun-Hwan Jeong

Second, SalmonTE is not relevant with any version of genome index, it is mainly on TE sequences in RepBase. I recommend you to read our wiki page - https://github.com/LiuzLab/SalmonTE/wiki/How-to-build-a-customized-index to understand --te_only option.

Best,

Hyun-Hwan Jeong