...
We can do this filtering on the hg19_rnaseq_mirnaseq_intersect.bed
file we just created using bedtools intersect.
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cd $SCRATCH/core_ngs/intersect/
cat hg19_rnaseq_mirnaseq_intersect.bed | awk 'BEGIN{FS="\t";OFS="\t";}{if ($6 == "+"){print}}' | more
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You could also insist on columns 6 and 12 both being the plus strand as such:
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cd $SCRATCH/core_ngs/intersect/
cat hg19_rnaseq_mirnaseq_intersect.bed | awk 'BEGIN{FS="\t";OFS="\t";}{if ($6 == "+" && $12 == "+"){print}}' | more
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