bedtools makewindows 生成滑窗区域文本
2019-07-09 本文已影响0人
Amy_Cui
学习目的，就为了得到这个文本，命令：bedtools makewindows -g genome.chr.ln -w 200000 >200K.genome.3col；当然你还可以写一个单行命令来处理。我这里用的是bedtools软件。
genome.chr.ln示例.png
结果文件：相隔200k的bed文件
安装
官网各种安装方法
conda 安装
$ conda install bedtools
$ bedtools --help
bedtools is a powerful toolset for genome arithmetic.
Version: v2.28.0
About: developed in the quinlanlab.org and by many contributors worldwide.
Docs: http://bedtools.readthedocs.io/
Code: https://github.com/arq5x/bedtools2
Mail: https://groups.google.com/forum/#!forum/bedtools-discuss
Usage: bedtools <subcommand> [options]
...
源码安装
$ wget https://github.com/arq5x/bedtools2/releases/download/v2.28.0/bedtools-2.28.0.tar.gz
$ tar -zxvf bedtools-2.28.0.tar.gz
$ cd bedtools2
$ make
系统安装
需要管理员权限
Fedora / Centos。Adam Huffman为bedtools创建了一个Red Hat软件包，以便可以使用Fedora软件包管理器“yum”轻松安装最新版本。它应该适用于Fedora 13,14和EPEL5 / 6（适用于Centos，Scientific Linux等）。
yum install BEDTools
于Debian / Ubuntu。Charles Plessy还维护着一个Debian软件包，可以在Ubuntu等衍生产品中找到。非常感谢Charles这样做。
apt-get install bedtools
自制。Carlos Borroto已经在OSX的bedtools包管理器上提供了BEDTools。
brew tap homebrew/science
brew install bedtools
MacPorts。或者，MacPorts端口系统可用于在OSX上安装BEDTools。
port install bedtools
makewindows的使用
查看bedtools makewindows 的帮助文档，最下面是示例，非常实用，看完就会了
准备-g文件
samtools dict /public/reference/genome/hg38/hg38.fa >hg38.fa.dict
# One can use the UCSC Genome Browser's MySQL database to extract: chromosome sizes. For example, H. sapiens:
# mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e \
# "select chrom, size from hg19.chromInfo" > hg19.genome
cat hg38.fa.dict|grep -v '^@HD'|sed 's/:/\t/g'|cut -f 3,5 >genome.chr.ln
bedtools makewindows -g genome.chr.ln -w 200000 >200K.genome.3col
结束我的需求！
帮助文档示例写的很明白
*****
*****ERROR: Need -g (genome file) or -b (BED file) for interval source.
*****
*****
*****ERROR: Need -w (window size) or -n (number of windows).
*****
Tool: bedtools makewindows
Version: v2.28.0
Summary: Makes adjacent or sliding windows across a genome or BED file.
Usage: bedtools makewindows [OPTIONS] [-g <genome> OR -b <bed>]
[ -w <window_size> OR -n <number of windows> ]
Input Options:
-g <genome>
Genome file size (see notes below).
Windows will be created for each chromosome in the file.
-b <bed>
BED file (with chrom,start,end fields).
Windows will be created for each interval in the file.
Windows Output Options:
-w <window_size>
Divide each input interval (either a chromosome or a BED interval)
to fixed-sized windows (i.e. same number of nucleotide in each window).
Can be combined with -s <step_size>
-s <step_size>
Step size: i.e., how many base pairs to step before
creating a new window. Used to create "sliding" windows.
- Defaults to window size (non-sliding windows).
-n <number_of_windows>
Divide each input interval (either a chromosome or a BED interval)
to fixed number of windows (i.e. same number of windows, with
varying window sizes).
-reverse
Reverse numbering of windows in the output, i.e. report
windows in decreasing order
ID Naming Options:
-i src|winnum|srcwinnum
The default output is 3 columns: chrom, start, end .
With this option, a name column will be added.
"-i src" - use the source interval's name.
"-i winnum" - use the window number as the ID (e.g. 1,2,3,4...).
"-i srcwinnum" - use the source interval's name with the window number.
See below for usage examples.
Notes:
(1) The genome file should tab delimited and structured as follows:
<chromName><TAB><chromSize>
For example, Human (hg19):
chr1 249250621
chr2 243199373
...
chr18_gl000207_random 4262
Tips:
One can use the UCSC Genome Browser's MySQL database to extract
chromosome sizes. For example, H. sapiens:
mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e \
"select chrom, size from hg19.chromInfo" > hg19.genome
Examples:
# Divide the human genome into windows of 1MB:
$ bedtools makewindows -g hg19.txt -w 1000000
chr1 0 1000000
chr1 1000000 2000000
chr1 2000000 3000000
chr1 3000000 4000000
chr1 4000000 5000000
...
# Divide the human genome into sliding (=overlapping) windows of 1MB, with 500KB overlap:
$ bedtools makewindows -g hg19.txt -w 1000000 -s 500000
chr1 0 1000000
chr1 500000 1500000
chr1 1000000 2000000
chr1 1500000 2500000
chr1 2000000 3000000
...
# Divide each chromosome in human genome to 1000 windows of equal size:
$ bedtools makewindows -g hg19.txt -n 1000
chr1 0 249251
chr1 249251 498502
chr1 498502 747753
chr1 747753 997004
chr1 997004 1246255
...
# Divide each interval in the given BED file into 10 equal-sized windows:
$ cat input.bed
chr5 60000 70000
chr5 73000 90000
chr5 100000 101000
$ bedtools makewindows -b input.bed -n 10
chr5 60000 61000
chr5 61000 62000
chr5 62000 63000
chr5 63000 64000
chr5 64000 65000
...
# Add a name column, based on the window number:
$ cat input.bed
chr5 60000 70000 AAA
chr5 73000 90000 BBB
chr5 100000 101000 CCC
$ bedtools makewindows -b input.bed -n 3 -i winnum
chr5 60000 63334 1
chr5 63334 66668 2
chr5 66668 70000 3
chr5 73000 78667 1
chr5 78667 84334 2
chr5 84334 90000 3
chr5 100000 100334 1
chr5 100334 100668 2
chr5 100668 101000 3
...
# Reverse window numbers:
$ cat input.bed
chr5 60000 70000 AAA
chr5 73000 90000 BBB
chr5 100000 101000 CCC
$ bedtools makewindows -b input.bed -n 3 -i winnum -reverse
chr5 60000 63334 3
chr5 63334 66668 2
chr5 66668 70000 1
chr5 73000 78667 3
chr5 78667 84334 2
chr5 84334 90000 1
chr5 100000 100334 3
chr5 100334 100668 2
chr5 100668 101000 1
...
# Add a name column, based on the source ID + window number:
$ cat input.bed
chr5 60000 70000 AAA
chr5 73000 90000 BBB
chr5 100000 101000 CCC
$ bedtools makewindows -b input.bed -n 3 -i srcwinnum
chr5 60000 63334 AAA_1
chr5 63334 66668 AAA_2
chr5 66668 70000 AAA_3
chr5 73000 78667 BBB_1
chr5 78667 84334 BBB_2
chr5 84334 90000 BBB_3
chr5 100000 100334 CCC_1
chr5 100334 100668 CCC_2
chr5 100668 101000 CCC_3
...
