bedtools no strand information - fasta file

Question

[pingu77]

Hello,

I want to extract some regions based on my bed file where I have chr, start, end (no strand information).

I am using bedtools getfasta, but if I don't specify the -s option, does it give me in output the reverse complement if the sequence is on the - strand?

thank you in advance

Best

Answer 1

[iraun]

The manual says that the strand information is ignored by default (unless you specify -s). So if you do not have strand information, the sequences will be returned in forward orientation. To be 100% sure it is always convenient to run a small test with a dummy fasta sequence and dummy bed file (as the examples you can see in the manual).