Assembly of Genomes

From mapping and variant calling to denovo assembly of genomes

1. Grepping genes from FASTA reference files # #1. Create a bed file with the location (chromosome, start position, end position) # #Using this bed file, can extract from fasta file using bedtools # bedtools getfasta -fi ~/REFERENCE/GENOME/PATH/file.fasta -bed ~/BED/FILE/Forgene.bed > OUTPUT_FILENAME.fa