Hello, I have a gff3 file. I'm using the following command line to extract sequences for each CDS:
bedtools getfasta -fi pseudomolecules.fasta -bed all.gff3 -fo CDS.fa chr1A rnaseq CDS 992 1945 . + 0 mRNA_1 chr1B rnaseq CDS 72477 25295 . + 0 mRNA_7 chr2D rnaseq CDS 13 725 . + 0 mRNA_6
1)Is there a way to get the last lines (mRNA_1) added to the header as well? my header is >chr1A:992-1945 and my wanted header is >chr1A:992-1945:mRNA_1
2) Is this command line going to take me the coordinates from each chromosome, because I have one fasta file containing all chromosomes.