Convert per base bedgraph to Bed format

Question

[bioyas]

Hi everyone,

I have a bed graph file which contains par base intervals. I would like to convert this file to Bed format where we have longer intervals. Here is the BedGraph file.

PvP01_01_v1   0     1   0
PvP01_01_v1   1     2   3.39882
PvP01_01_v1   2     5   3.81385
PvP01_01_v1   5     7   2.81385
PvP01_01_v1   7     10  3.55081

Is there any tool that does the job?

Thanks,

Answer 1

[mmmmcandrew]

You can use bedtools merge. On your example data, this will create a single entry in the format:

PvP01_01_v1   0   10

It's not clear whether the information in your fourth column here is relevant for your future analyses, but you will likely lose that information.

[Carlo Yague]

Just for information, it is possible to retain the information of the 4th column by using bedtools merge options -c 4 and -o mean (among other possible operators). It will take the mean of the original 4th column values that overlap the new interval.

[mmmmcandrew]

Hell yea, thanks Carlo!

Answer 2

[Alex Reynolds]

Convert to sorted bed:

$ awk -v FS="\t" -v OFS="\t" '{ print $1, $2, $3, ".", $4 }' in.bedGraph | sort-bed - > in.bed 

To merge:

$ bedops --merge in.bed > merged_intervals.bed

To map and apply signal operations:

$ bedmap --echo --sum merged_intervals.bed in.bed > signal_sum_over_merged_intervals.bed
$ bedmap --echo --mean merged_intervals.bed in.bed > signal_mean_over_merged_intervals.bed
$ bedmap --echo --median merged_intervals.bed in.bed > signal_median_over_merged_intervals.bed

Etc.

If you don't need to preserve signal, you can just strip it out:

$ sort-bed <(cut -f1-3 in.bedGraph) | bedops --merge - > merged_intervals.bed

If doing set operations that require signal, however, the ideal is to generate five-column BED, in order to follow UCSC specifications.

Ref:

• https://bedops.readthedocs.io/en/latest/content/reference/file-management/sorting/sort-bed.html
• https://bedops.readthedocs.io/en/latest/content/reference/set-operations/bedops.html#merge-m-merge
• https://bedops.readthedocs.io/en/latest/content/reference/statistics/bedmap.html#score-operations