How to build a local index

[zya226]

Dear Hyun-Hwan Jeong,

I am trying to build my own SalmonTE index. In the previous post, I found this link https://github.com/hyunhwaj/SalmonTE/wiki/How-to-build-a-customized-index. However, it did not work. Could you please tell me how to build the SalmonTE index if I have my own fasta file and gtf file?

Thanks in advance, Yong

[hyunhwan-jeong]

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

[zya226]

Dear Hyun-Hwan,

Thank you for your quick response.

I am interested in hg38 gene features and ERVs expression of 339 RNA-seq samples. I have my own defined ERVs that are different from those in the public databases. So I would like to build my own index. I have extracted the sequences for my ERVs (fasta file). What should I do for the next step? The previous post mentioned the sequence name should have specific name rule (like name/family). Beside that, any other things I should pay attention?

Best, Yong

[hyunhwan-jeong]

@zya226,

Sorry for my late response, could you send your FASTA file to jeong.compbio@gmail.com?

Thank you,

Hyun-Hwan Jeong

[zya226]

Hi Hyun-Hwan,

Sorry, I just saw your email. I have sent my fasta file of transposons that I am interested in to your email.

Thanks, Yong

[hyunhwan-jeong]

Hi @zya226,

These days were busy days for me, and I had no time to take a look, I will respond to you soon! Sorry for the delay.

[zya226]

Sure, thanks! Please let me know when you have a chance to take a look.