Takes BED file of circRNA splice sites and creates a FASTA file of their junctions
Transforms BED6 files like this:
chrI 1 15 circID 0 +
to FASTA files like this:
>circID::chrI:1-15(+)
cctaagcctaagcc
to junction FASTA files like this automatically:
>circID::chrI:1-15(+)
ctaagccCCTAAGC
Run this command in your terminal:
sh primer_maker.sh test.bed ce11.fa
Copy & paste these commands in your terminal:
git clone https://github.com/alexandruioanvoda/junction-fasta-maker
cd junction-fasta-maker
chmod +x primer_maker.sh
BEDtools, awk and tr.