File GTF em file fasta: Extracting fasta sequences based on coordinates (BED/bedGraph/GFF/VCF/EncodePeak file)

Hello, I made the transcriptome assemblies with Cufflinks (GFF), but I need to extract this sequence in Fasta format, for further analysis outside the platform. How to make?

1 Like

Hi @Thiely,
you can use the gffread tool in order to generate the FASTA file. It requires to use as input both the GFF file generated by Cufflinks and the reference genome.


1 Like

@gallardoalba can’t, it’s never successful. Know how I can select step-by-step. Can you help me please

@gallardoalba url:

1 Like


Didn’t notice that you have shared your history, sorry!

It looks like this is working now using an alternative method. :slight_smile:

For others reading, the tool to extract fasta based on coordinates is: bedtools GetFastaBed use intervals to extract sequences from a FASTA file


All of the tuxedo tools are deprecated at

You can try at instead.

Be aware that the extracted fasta will be based on the genomic base pairs. Meaning, any variation in your reads (snps) would not be captured. This usually doesn’t matter – but the alternative is to actually assemble the reads (tool: Trinity). You can search this forum with the keyword for that tool to find prior Q&A and tutorial links for the how-to. Or, review here:

1 Like