'cDNA_match' instead of contig names

[jeboyen]

When cds gets extracted, getfasta takes 'cDNA match' as names instead of the actual fasta names, because the gff3 file has 'cDNA match' in its 'name' column. To prevent this, we can add the following line.

Replace 'cDNA match' with contig names

awk -v OFS='\t' '$3=$1' "$file"2.gff3 > "$file"3.gff3

and use this file as input to getfasta

Extract cds using bedtools (results in each exon appearing on as a separate sequence)

bedtools getfasta -fi "$file" -bed "$file"3.gff3 -name -s > "$file"_int1.fa

--> Still one problem: if multiple genes occur on the same contig, they will be merged together, how to solve that?