Can BEDOps bedmap retain strand information?
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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.

Bedops bedmap • 839 views
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