Hi Everyone,

How can I extract promoter sequences (ca. 1000bp upstream TSS) in multi-fasta format from genome (also multi-fasta with scaffolds) using information from corresponding GFF file? I've already tried to use GFF-Ex tool, however it didn't help (finished with errors). It is tobacco genome (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/715/135/GCF_000715135.1_Ntab-TN90/).

Does anyone know some other tools for this?

Thanks,
Finally, I've solved this problem by combining samtools, bedtools as well as custom R script. The pipline placed into bash script is available [here](https://github.com/RimGubaev/extract_promoters).