A small issue is that the file that I think it first references is saccer3.fa.fai, not sc.fa.fai (as that doesn't exist so far, given instructions). Second, there aren't instructions to obtain genes.gff (at least as far as I'm aware, I haven't found any in the ChIP-Seq section); I went here, via the link from the handbook and clicking on the "Genome" link under "Related Information", and obtained the gff file there. However, running the above command gives this error:
ERROR: chrom "NC_001133.9" not found in genome file. Exiting.
Wondering if you would be able to include where the gff file comes from
Hello,
In this part, there is a command
bedtools flank -g refs/sc.fa.fai -l 1000 -r 0 -s -i refs/genes.gff > flanked.gffA small issue is that the file that I think it first references is saccer3.fa.fai, not sc.fa.fai (as that doesn't exist so far, given instructions). Second, there aren't instructions to obtain
genes.gff(at least as far as I'm aware, I haven't found any in the ChIP-Seq section); I went here, via the link from the handbook and clicking on the "Genome" link under "Related Information", and obtained the gff file there. However, running the above command gives this error:ERROR: chrom "NC_001133.9" not found in genome file. Exiting.Wondering if you would be able to include where the gff file comes from