Hi. Thanks for joining the forum.
To use BEDOPS in a strand-sensitive way, you'll have to break your analysis up a bit. If your strand information is in the 6th column, for example:
awk '$6 == "+"' myfile.bed \
| bedmap --echo --count .... \
> result.forward-strand.bed
Do the same on the opposing strand, and, if you'd like, you can glue things back together using bedops -u into a final result.
By default, bedmap will map anything in your second file that overlaps the first file's region by 1 bp or more (not necessarily the 5' end). This seems to do what you want by default, but you can add the --bp-ovr 1 flag explicitly if you like.
When extending a region, you'll want to use bedops --range since you want a non-symmetrical padding. The --range option with bedmap is a bit different and it's a symmetrical thing.
I'll pretend that you have two files, both of which have strand information in the 6th column. And, I'll pretend that you want to add 10 bp of upstream padding.
a.bed
b.bed
awk '$6 == "+"' a.bed | bedops -u --range -10:0 > a.plus.bed
awk '$6 == "-"' a.bed | bedops -u --range 0:10 > a.minus.bed
You would need to parse out per-strand information from b.bed if you want strand-sensitive results. So, your original 2 files becomes 4.
bedmap --echo --count a.plus.bed b.plus.bed > plus.final.bed
bedmap --echo --count a.minus.bed b.minus.bed > minus.final.bed
If you want these results in one file at the end:
bedops -u plus.final.bed minus.final.bed > final.answer.bed
Hope that helps. Most important to everything in BEDOPS is that your files are sorted properly using the sort-bed program - make sure to do that for a.bed and b.bed before anything else. The other outputs you generate will be in sorted order, so you don't have to do that again.
Shane
