I am searching for new antimicrobial peptides and I don't have many skills in bioinformatics, so I want to know how to use these software packages to identify candidate coding regions within transcript sequences.
Dear Alice,
Your question is a bit unspecific. If you want to know how a bioinformatics tool works, just google it and find a tutorial (here for transdecoder https://github.com/TransDecoder/TransDecoder/wiki).
Of course, this may not help a lot if you're starting with bioinformatics. Therefore I would need to know what kind of data you're working with.
Do you have RNAseq raw reads and want to assemble a transcriptome (which at some point will use transdecoder to detect open reading frames (ORFs) in your transcriptome assembly)?
If you want to assemble a transcriptome and directly analyse it, TRINITY would be my choice. You can follow the process from raw RNAseq reads to a de novo assembled transcriptome here
https://github.com/griffithlab/rnaseq_tutorial/wiki/Trinity-Assembly-And-Analysis and here
https://github.com/trinityrnaseq/trinityrnaseq/wiki/Genome-Guided-Trinity-Transcriptome-Assembly
You can learn a lot of basic bioinformatics by doing this process, but a basic bash course and a strong linux computer, or cluster are a requirement.
I hope this helps.
Cheers
https://www.google.com/url?sa=t&source=web&rct=j&url=https://www.biobam.com/predicting-coding-regions-within-transcripts-in-omicsbox-with-transdecoder/&ved=2ahUKEwix2YHM9rPtAhVHRBUIHS1JDOYQFjAAegQIAxAB&usg=AOvVaw17FXg3k1IHha1PeLuYyaqh&cshid=1607067688199
Thank you Mark for your answer. Actually I took the transcriptome sequences from NCBI and they are raw reads so I think that I have to follow what you have told me. Thanks again
Busayo, I tried working with omicsbox, but It always gives me a messeage " The prediction process was failed". I don't know what's the problem.
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