Extract transcript fasta using gff

Question

[boczniak767]

Hi,

is there simple way to extract fasta sequences of transcripts using genome fasta and gff?

I came across gffread which propose command gffread -w transcripts.fa -g /path/to/genome.fa transcripts.gtf. I just don't know, what this gff file has to contain. Exons, all features,...

The second possibility is mapToTranscript from GenomicFeatures R package. The manual is just quite complicated and I don't know steps to retrieve the transcripts.

Has anybody have any experience with such procedure?

Answer 1

[Juke34]

gffread is quite straightforward. It has to contain exons.

You might consider agat_sp_extract_sequences.pl from AGAT

Look at here for examples: Extracting genomic feature sequences from GTF/GFF files with AGAT

[boczniak767]

Thanks, indeed gffread seems to work perfect. I'm just checking results. Also thanks for link to AGAT.