如何合并两个或多个bed files

目的：把两组bed files 分别pool成一个bed file，而且叠加到序列区间要merge起来。
合并：cat *.bed > output.bed
软件：需要 bedtools
issue：当merge bed files时候出现了error，
ERROR: input file: (oLT.pooled.broadPeak) is not sorted by chrom then start. The start coordinate at line 2 is less than the start at line 1

解决办法：bedfile 如果想进行bedtools merge需要先sort。

1. 把reps pool到一起

[ye.liu@n201 removed_01_02_10]$ cat *iMT* > ./pooled/iMT.pooled.broadPeak
[ye.liu@n201 removed_01_02_10]$ cat *oLT* > ./pooled/oLT.pooled.broadPeak

2. 参考下面例子进行sort

$ more foo.bed
chr1    1       2
chr4    7       8
chrX    100     101
chr11   9       100
chr11   9       99
chr20   11      12
chr2    3       4
chr3    5       6

chr start end 都升序排列

$ sort -k1,1n -k2,2n -k3,3n foo.bed
chr1    1    2
chr2    3    4
chr3    5    6
chr4    7    8
chr11    9    99
chr11    9    100
chr20    11    12
chrX    100    101

这样chr start 升序排列

$ sort -k1,1n -k2,2n foo.bed
chr1    1    2
chr2    3    4
chr3    5    6
chr4    7    8
chr11    9    100
chr11    9    99
chr20    11    12
chrX    100    101

我做的，

[ye.liu@n201 pooled]$ sort -k1,1n -k2,2n -k3,3n iMT.pooled.broadPeak > sort.iMT.pooled.broadPeak
[ye.liu@n201 pooled]$ sort -k1,1n -k2,2n -k3,3n oLT.pooled.broadPeak > sort.oLT.pooled.broadPeak

另一种这样子比较好，

[ye.liu@n201 pooled]$ sortBed -i iMT.pooled.broadPeak > sort.iMT.pooled.broadPeak
[ye.liu@n201 pooled]$ sortBed -i oLT.pooled.broadPeak > sort.oLT.pooled.broadPeak
[ye.liu@n201 pooled]$ bedtools merge -i sort.iMT.pooled.broadPeak > pool.sort.iMT.pooled.broadPeak
[ye.liu@n201 pooled]$ bedtools merge -i sort.oLT.pooled.broadPeak > pool.sort.oLT.pooled.broadPeak