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?