The below awk is supposed filter $8 of example.txt using the each line in gene.txt . I think it is but why is it renumbering the 1,2,3 in $1 to 28,29,394? I have attached the data as it is large, example.txt is the file to be searched, gene.txt has the lines to match, and filtered.txt is the current output. The desured output is just that but with $1 or R_Index sequentially numbered. Thank you :).
awk
awk 'NR==FNR{for (i=1;i<=NF;i++) a[$i];next} FNR==1 || ($8 in a)' gene.txt example.txt | awk '{split($2,a,"-"); print a[1] "\t" $0}' | cut -f2-> filtered.txt
