Sorting the BEd File

Question

[rohitsatyam102]

Hi all

I was trying to sort BED file using the following command sort -k1,1 -k2,2n in.bed > in.sorted.bed The description of bedtools closest here says

bedtools closest requires that all input files are presorted data by chromosome and then by start position

However I am getting the outcome as follows:

• chr22 38143248 38143734
• chr2 238168767 238169127
• chr22 38614588 38614867
• chr2 239347857 239348510
• chr22 39631244 39631333
• chr22 39686679 39687117

I am unable to understand why chr2 coordinates are sorted between chr22. I tried understanding how the sort -k options works from here. But It's unclear to me whether what I understand is correct or not.

Is it like in -k1,1, k1 sorts the results by values present in 1st column (chr here) and ,1 uses first character i.e c . Please help me understand it. Also what does n does to the sorting.

[Pierre Lindenbaum]

what is the output of tr "\t" "#" < in.bed | head ?

Also what does n does to the sorting.

http://man7.org/linux/man-pages/man1/sort.1.html

Answer 1

[rohitsatyam102]

Hi @Pierre

I found my mistake just now. I was using 2 in place of 2n. And that made all the difference.