bedtools multiinter strange behavior (on sorted files)

[shmuel...@gmail.com]

Hi,

The following (sorted) input

> cat ttt1.bed

chr11   1       1000

X       1       1000

> cat ttt2.bed

chr12   2000    3000

X       500     600

produces no overlap.

> bedtools multiinter -i ttt1.bed ttt2.bed

chr11   1       1000    1       1       1       0

X       1       1000    1       1       1       0

chr12   2000    3000    1       2       0       1

X       500     600     1       2       0       1

Changing "X" to "chrX" gives the correct result. 

chr11   1       1000    1       1       1       0

chr12   2000    3000    1       2       0       1

chrX    1       500     1       1       1       0

chrX    500     600     2       1,2     1       1

chrX    600     1000    1       1       1       0

[Aaron Quinlan]

Bedtools assumes that the chromosome column is sorted lexicographically (e.g., with UNIX `sort -k1,1`). Under this assumption, your input files are not sorted lexicographically by chromosome.

You should be fine if you always do: `sort -k1,1 -k2,2n x.bed > x.sorted.bed` before using this tool.

Best,

Aaron

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[Sam]

Thanks.

Actually, the files were sorted in the manner you have suggested.  Only thing, they were sorted when the locale was en_US.UTF-8, which has produced the sorting order I have posted.

Changing the locale settings LC_ALL=C has fixed the sorting. 

Best, 

Sam