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apcamargo / RNAsamba

A tool for computing the coding potential of RNA transcript sequences using deep learning classification model
https://rnasamba.lge.ibi.unicamp.br/
GNU General Public License v3.0
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Using as a beginner #13

Closed resulkiymaz1 closed 3 years ago

resulkiymaz1 commented 3 years ago

Hello there!

I have found this useful tool recently and I'm not good at with bioinformatics. So I made differential gene expression by Hisat2 and assemled all the transcript with stringtie. I want to calculate my transcrips' coding potential but I don't know how to change my gtf file to fasta file including the transcrips' sequences. Can you help me for this instance?

Best Regards..

apcamargo commented 3 years ago

Sure!

If you used StringTie you should have the genome FASTA file. You can use gffread to extract the transcripts from it using a GTF:

gffread -w transcripts.fa -g /path/to/genome.fa transcripts.gtf

Let me know if this solves your issue.

resulkiymaz1 commented 3 years ago
Thank you : Antônio Camargo  Windows 10 için Posta ile gönderildi Kimden: Antônio CamargoGönderilme: 19 Haziran 2021 Cumartesi 22:55Kime: apcamargo/RNAsambaBilgi: resulkiymaz1; AuthorKonu: Re: [apcamargo/RNAsamba] Using as a beginner (#13) Sure!If you used StringTie you should have the genome FASTA file. You can use gffread to extract the transcripts from it using a GTF:gffread -w transcripts.fa -g /path/to/genome.fa transcripts.gtf—You are receiving this because you authored the thread.Reply to this email directly, view it on GitHub, or unsubscribe.