I am trying to extract the CDS sequences from a genome in fasta format. I have a gtf file.
Googleing around it seems that the gffread command in the cufflinks package can do this.
However when I try to implement it I just get blank files.
Following the documentation I tried this:
gffread transcripts.gtf -x extracted_transcripts.fa -g genome.fasta
but I just got a file with nothing in it
then because most cufflinks programs seem to like having the options first and inputs second I tried this:
gffread -x extracted_transcripts.fa -g genome.fasta transcripts.gtf
same result. What am I missing?
I am mistaken. I assumed that because my *.gtf file was produced by cufflinks I could use gffread -x as gffread is part of the same suite of programs as cufflinks. This is not the case as cufflinks does not identify CDS and does not go above the transcript level.
Following this How To Extract Cds And Protein Sequences From Cufflinks Transcripts.Gtf File? I an going to give TransDecoder a go.
Even with cufflinks out file transcript.gtf, -w option should work.
gffread transcripts.gtf -g genome.fa -o transcripts.gff -w transcripts.fa
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This works for me:
gffread -g genome.fa -x CDS.fa annotation.gtfmake sure you have a valid gtf / fa / fasta file and they are using the same format for chromosomes. It would help if you paste in the top couple lines of each file.