problem with bedtools complement: how to extract strand information?
Hi everyone,
I have a minor trouble when using bedtools complement. My gff3 file contains Chr start end strand etc. information. I want to use bedtools complement to extract other regions, however, the command bedtools complement -i gff_file -g genome_file gives me three columns: Chr, start, end. The output does not have strand information.
Thank you very much
2 answers
Taking the complement of both strands separately worked for me.
grep -v '+$' sorted_gff_file | bedtools complement -i stdin -g genome_file | sed 's/$/\t-/' > complement_file
grep '+$' sorted_gff_file | bedtools complement -i stdin -g genome_file | sed 's/$/\t+/' >> complement_file
You can sort the complement file after this.
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deepali.kundnani •
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This tool would give you the regions of your
genome_filewhich are not in yourgff_file. What strand you expect from output?