要用bedtools了， 当然要熟悉bed文件格式

一共十二列

1， chrom 不解释

2， start, 0-based

3， end, 说明书说是1-based, include。 不如理解为0-based, exclude

4, name, genome feature 的名字

5， score, 没什么用好像

6， strand, +or-

7, thickstart, the starting position at which the feature is drawn thickly

8, thickend , the ending positiion at which the feature is drawn thickly

9, intemRGB, an RGB value

10, blockcount, the number of blocks(exons) in the bed line

11, blocksizes, a comma-separated list of the block sizes

12, blockstarts, a comma-separated list of block starts

并不是每列对bedtools都有用。

BED3 指前三列， chrom, start, end

BED4 前四列 ， chrom start end name

BED5 前五列， chrom start end name score

BED6 前六列， chrom start end name score strand

BED12 所有列

除了以上几种，bedtools还定义了bedpe format:

We have defined a new file format (BEDPE) in order to concisely describe disjoint genome features, such as structural variations or paired-end sequence alignments. We chose to define a new format because the existing “blocked” BED format (a.k.a. BED12) does not allow inter-chromosomal feature definitions. In addition, BED12 only has one strand field, which is insufficient for paired-end sequence alignments, especially when studying structural variation.

by freemao

FAFU.

free_mao@qq.com

BED format