目的：把兩組bed files 分別pool成一個(gè)bed file，而且疊加到序列區(qū)間要merge起來(lái)。
合并：cat *.bed > output.bed
軟件：需要 bedtools
issue：當(dāng)merge bed files時(shí)候出現(xiàn)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
解決辦法：bedfile 如果想進(jìn)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
- 參考下面例子進(jìn)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
這樣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
另一種這樣子比較好，
[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
