Multi-fasta file for gffread

Question

[Vitor1]

Hey Guys,

I'm having a problem trying to extract the transcripts from a merged StringTie .gtf file with gffread. I have downloaded the cDNA fastq file from ENSEMBL and tried to run the following command:

gffread -w transcripts.fa -g /path/to/genome.fa transcripts.gtf

However I'm getting the following result:

Warning: couldn't find fasta record for '1'! Error: no genomic sequence available (check -g option!).

What should I do in this case? Is this the right fastq file that I have tried?

Thanks

[GenoMax]

You need to provide genome file as input along with the GTF.

[Istvan Albert]

specifically this:

-g /path/to/genome.fa 

needs to be the actual path to the genome, what you have there is the example from the description.

But for the reference, the command extracts transcripts from a genome, based on transcript information in the GFT file.

You say you downloaded CDN FASTQ files from ENSEMBL ... that does not seem right. Do you mean FASTA file? Those files are not suited to extract transcripts with gffread. Make sure to study what the tools do.