bedtools intersect by position & stand not working even with common regions

Question

[Alewa]

i want to extract only sites (strand aware) that appear in both D-A-3_modpileup_5mC.chr1.bed and consensus_HighQual_motif_sites.bed but it's not working even though they have overlapping sites.

bedtools intersect -a D-A-3_modpileup_5mC.chr1.bed -b consensus_HighQual_motif_sites.bed -s

Here's common site with same strand

$ cat consensus_HighQual_motif_sites.bed | grep "3003225"
chr1    3003225 3003226 +

$ cat D-A-3_modpileup_5mC.chr1.bed | grep "3003226"
chr1    3003225 3003226 +       m       12      25.00   3       9       0       0       0       01
chr1    3003226 3003227 -       m       13      38.46   5       8       0       2       1       00
chr1    63003225        63003226        -       m       19      52.63   10      9       0       001       2
chr1    193003225       193003226       -       m       11      0.00    0       11      0       000       0

it's a bed file

cat -t consensus_HighQual_motif_sites.bed | head
chr1^I3003225^I3003226^I+
chr1^I3003226^I3003227^I-
chr1^I3003338^I3003339^I+
chr1^I3003339^I3003340^I-
chr1^I3003378^I3003379^I+
chr1^I3003379^I3003380^I-
chr1^I3003581^I3003582^I+
chr1^I3003582^I3003583^I-
chr1^I3003639^I3003640^I+
chr1^I3003640^I3003641^I-

[rfran010]

are you sure bedtools can handle the non-standard location of strand information?

[Alewa]

thanks for hint!