[SOLVED] How to get strand when extracting fasta sequences using bed file

How to get strand when extracting fasta sequences using bed file

I am trying to extract fasta sequences from a genome using a bed file (homemade). The bed file looks like this (tab separated):

LQNS02278165.1  13104710        13109495        +
LQNS02278165.1  9139127 9142308 +
LQNS02278165.1  13665793        13666495        +
LQNS02278165.1  9143024 9144041 +
LQNS02278165.1  9221339 9222957 -
LQNS02278165.1  9220085 9220713 -
LQNS02278165.1  12608731        12609200        +
LQNS02278165.1  9144041 9144734 +
LQNS02278165.1  13666286        13666752        +
LQNS02278165.1  13655380        13655764        +

I am running bedtools getfasta with option force strandedness (-s) but this is not working. The output I get is not taking the strand into account as it should. Any suggestions ?

bedtools getfasta -s  -fo strand_genome.fa -fi genome.fa -bed f.blast_genome.bed -fullHeader

>LQNS02278165.1:13104710-13109495()
AAAAAAA....
>LQNS02278165.1:9139127-9142308()
AAAAAAA....
>LQNS02278165.1:13665793-13666495()
AAAAAAA....
>LQNS02278165.1:9143024-9144041()
AAAAAAA....
>LQNS02278165.1:9221339-9222957()
AAAAAAA....

THANKS!

Solution

According to bed format, the strand is on the 6th column, so in your example just move the strand to the 6th column:

cat test.fa
>chr01
ACCGGTT

cat test.bed
chr01   0   4   .   .   +
chr01   0   4   .   .   -

bedtools getfasta -s -fi test.fa -bed test.bed
>chr01:0-4(+)
AACC
>chr01:0-4(-)
GGTT