This is my first post so please bear with me. I have about 2000 bed files that I would like to extract FASTA sequences from. I have been able to extract a single set of bed sequences using the following command:
.narrowPeak is a BED file.
bedtools getfasta -fi TAIR10_Chr.fasta -bed /copy_peaks/ABI5_col_v3h.narrowPeak > ABI5_col_v3h.fasta
within my copy_peaks folder there are 2000 other files I would like to perform this operation on. Any ideas?
The results will then be used in fimo, where again I will need to perform this operation on the extracted fasta files.