Entering edit mode
4.2 years ago
Tawny
▴
180
I am using bedmap
to bin my 6 column bed files that include strand in the 6th column.
This produces a binned bed file with only 4 columns, omitting the read name and strand column.
Is there a method within bedmap
that would allow me to retain the strand information?
Perhaps I need to go back to my binned reference and somehow include strand information in that?
Here is the full command I am using.
home/tools/BEDOPS/bin/bedmap \
--fraction-map 0.5 --ec --echo --skip-unmapped --sum --delim '\t' --prec 0 \
/home/tools/BEDOPS/hg38_chromSizes2_sort_500bpBins.bed \
/home/in_sort.bed \
> /home/out_sort_500bpBins.bed
My other option might be to just separate out my bed file into two files by strand, then bin, add a strand column to each separately binned file, and then combine the two bed files by concatenation.