extract entire header from BED file to FASTA
Hi,
Is there any way one can extract the entire header from a BED file while using bedtools getfasta
command and write it in the FASTA output ?
Have tried using bedtools getfasta -fi hg19.fa -bed file.bed -fo test.fasta -fullHeader
but it doesnt work somehow.
if this is the BED region:
chr1 152811364 152811709 annotation
the output
>chr1:152811364-152811709
ttatttatttatttatttatttatttttttattatactttaagttttagggtacatgtgcacattgtgc
should be
>chr1:152811364-152811709 | annotation
ttatttatttatttatttatttatttttttattatactttaagttttagggtacatgtgcacattgtgc
any ideas.
Thanks.
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