Hello,
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?
Thank you!
•
written
by
biostart
1 answer
Another option:
$ closest-features --nearest RNA-seq.bed ChIP-seq-peaks.bed > output.bed
Features are put onto one line.
Depending on the state of inputs, it may be worthwhile to sort, e.g.:
$ sort-bed < RNA-seq.unknown-sort.bed > RNA-seq.bed
$ sort-bed < ChIP-seq-peaks.bed.unknown-sort.bed > ChIP-seq-peaks.bed
Also make sure your inputs don't have any weird line endings, e.g.:
$ cat -e RNA-seq.unknown-line-endings.bed | head
$ cat -e ChIP-seq-peaks.unknown-line-endings.bed | head
If you have more than dollar signs at the end of each line ($) then use tools like sed or dos2unix to preprocess or convert files as needed.
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