some general questions

[Dimitris Hatzopoulos]

https://github.com/TransDecoder/TransDecoder/wiki i am new to this so sorry for noobie questions. I am trying deNovo assembly using Trinity from a single fastq file, so i got a file named Trinity.fasta. Wanted to ask when doing this command =

gtf_genome_to_cdna_fasta.pl transcripts.gtf test.genome.fasta > transcripts.fasta, transcripts.gtf is which file? test.genome.fasta is the Trinity.fasta? 

[Brian Haas]

Hi,

The gtf_genome_to_cdna_fasta.pl is used to convert genome-based transcript structure annotations into a fasta file.  You wouldn't do this with Trinity.... instead it would be for use with a tool like StringTie, Cufflinks, etc.

You could take another look at the wiki and the different examples that are included with TransDecoder, and let me know what it is that you're aiming to do.

best,

~b

On Fri, Feb 7, 2020 at 5:30 AM Dimitris Hatzopoulos <dimitr...@gmail.com> wrote:

https://github.com/TransDecoder/TransDecoder/wiki i am new to this so sorry for noobie questions. I am trying deNovo assembly using Trinity from a single fastq file, so i got a file named Trinity.fasta. Wanted to ask when doing this command =

gtf_genome_to_cdna_fasta.pl transcripts.gtf test.genome.fasta > transcripts.fasta, transcripts.gtf is which file? test.genome.fasta is the Trinity.fasta? 

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Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas