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。
- 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
- 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
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