使用bedtools划分各种条件的bin

• 参考染色体大小文件chrom.size

chr1    100
chr2    150

• 将染色体划分为20bp为一个bin的区间

$ bedtools makewindows -g  chrom.size -w 20
chr1    0   20
chr1    20  40
chr1    40  60
chr1    60  80
chr1    80  100
chr2    0   20
chr2    20  40
chr2    40  60
chr2    60  80
chr2    80  100
chr2    100 120
chr2    120 140
chr2    140 150

• 将染色体划分成20bp为一个bin滑动距离为10bp的区间

$  bedtools makewindows -g  chrom.size -w 20 -s 10
chr1    0   20
chr1    10  30
chr1    20  40
chr1    30  50
chr1    40  60
chr1    50  70
chr1    60  80
chr1    70  90
chr1    80  100
chr1    90  100
chr2    0   20
chr2    10  30
chr2    20  40
chr2    30  50
chr2    40  60
chr2    50  70
chr2    60  80
chr2    70  90
chr2    80  100
chr2    90  110
chr2    100 120
chr2    110 130
chr2    120 140
chr2    130 150
chr2    140 150

• 将每条染色体划分为5个相同大小的窗口

$ bedtools makewindows -g chrom.size -n 5
chr1    0   20
chr1    20  40
chr1    40  60
chr1    60  80
chr1    80  100
chr2    0   30
chr2    30  60
chr2    60  90
chr2    90  120
chr2    120 150

• 将给定BED文件中的每个间隔划分为5个大小相等的窗口

$ cat chrom.size.bed 
chr1    1   100
chr2    1   150

$ bedtools makewindows -b chrom.size.bed -n 5
chr1    1   20
chr1    20  39
chr1    39  58
chr1    58  77
chr1    77  100
chr2    1   30
chr2    30  59
chr2    59  88
chr2    88  117
chr2    117 150

• 将给定BED文件中的每个间隔划分为3个大小相等的窗口, 并且在最后一列加上属于第几个bin，这对于ChIP-seq、BS-seq等这种需要绘制metaplot的图时候，作用特别好。

$ cat chrom.size_3col.bed 
chr1    1   100 A
chr1    200 300 B
chr1    350 400 C

$ bedtools makewindows -b chrom.size_3col.bed -n 3 -i winnum
chr1    1   34  1
chr1    34  67  2
chr1    67  100 3
chr1    200 233 1
chr1    233 266 2
chr1    266 300 3
chr1    350 366 1
chr1    366 382 2
chr1    382 400 3

$ bedtools makewindows -b chrom.size_3col.bed -n 3 -i srcwinnum
chr1    1   34  A_1
chr1    34  67  A_2
chr1    67  100 A_3
chr1    200 233 B_1
chr1    233 266 B_2
chr1    266 300 B_3
chr1    350 366 C_1
chr1    366 382 C_2
chr1    382 400 C_3

• 有时候需要区分正负方向呢？

$ bedtools makewindows -b chrom.size_3col.bed -n 3 -i winnum -reverse
chr1    1   34  3
chr1    34  67  2
chr1    67  100 1
chr1    200 233 3
chr1    233 266 2
chr1    266 300 1
chr1    350 366 3
chr1    366 382 2
chr1    382 400 1

• 结合上面生成以下？一般这种方式感觉作用不大。

$  bedtools makewindows -b chrom.size.bed -w 20 -s 10 -i winnum
chr1    1   21  1
chr1    11  31  2
chr1    21  41  3
chr1    31  51  4
chr1    41  61  5
chr1    51  71  6
chr1    61  81  7
chr1    71  91  8
chr1    81  100 9
chr1    91  100 10
chr2    1   21  1
chr2    11  31  2
chr2    21  41  3
chr2    31  51  4
chr2    41  61  5
chr2    51  71  6
chr2    61  81  7
chr2    71  91  8
chr2    81  101 9
chr2    91  111 10
chr2    101 121 11
chr2    111 131 12
chr2    121 141 13
chr2    131 150 14
chr2    141 150 15

• 使用awk进行均分

[qliu@node9 bedtools_test]$ awk -v num_win=5 '{len = $3-$2; size = len/num_win; \
>                             for (start=$2; start<$3; start+=size) \
>                                print $1"\t"start"\t"start+size}' chrom.size.bed

• bedtools makewindows参数：

Transcriptome analysis and bedtools
Question: Sliding window using gene position file
generating BED with sliding-windows intervals
strand-aware makewindows?

bedtools intersect -u -a $featureBED -b $signalBED | \
cat <(awk '($6 == "+")' | bedtools makewindows -b - -w $windowBin -i srcwinnum) \
      <(awk '($6 == "-")' | bedtools makewindows -b - -w $windowBin -i srcwinnum -reverse) > out.bed