Is there a way to ask bedtools to return both regions in one line (not in two lines)? See below.
I just run into a problem with bedtools closest. Here is the command:
bedtools closest -a RNA-seq.bed -b ChIP-seq-peaks.bed -d > output.bed
The RNA-seq file contains about 30 columns, starting with Chromosome, Start, End. The ChIP-seq-peaks file is in a classical bed format. Both files are sorted.
The resulting file has two lines per each initial line of the file RNA-seq.bed. The insersecting peak is added as a separate line. Is there a way to tell bedtools to not make a line break?