bam格式转bigWig

当我们需要在UCSC browser中可视化的时候，将bam文件转化为bigwig文件会更加方便。而deeptools中的bamCoverage可以方便的实现这个功能。

1. 安装

conda或者pip安装：

conda install -c bioconda deeptools
# 或者
pip install deeptools

github源代码安装：

 git clone https://github.com/deeptools/deepTools.git
wget https://github.com/deeptools/deepTools/archive/1.5.12.tar.gz
tar -xzvf
python setup.py install --prefix /User/Tools/deepTools2.0

一定要注意一下的依赖包必须满足要求：

如果不满足要求的话，bam2Coverage可能会引发如下错误：
"The XXX file does not have BAM or CRAM format"；
"ModuleNotFoundError: No module named 'numpy.core._multiarray_umath'"等等。

2. bam2Coverage

必需参数：

需指定输入文件，输出文件名。输出文件格式默认为bigwig，如果想输出bedgraph文件需指定。

非必需参数：

此外还有Read coverage normalization options和Read coverage normalization options，有具体需要可以查阅。

ChIP-seq的例子：

bamCoverage --bam a.bam -o a.SeqDepthNorm.bw \
    --binSize 10
    --normalizeUsing RPGC
    --effectiveGenomeSize 2150570000
    --ignoreForNormalization chrX
    --extendReads

RNA-seq的例子：

bamCoverage -b a.bam -o a.bw

当我们需要分离正负链时（单端）：

bamCoverage -b a.bam -o forward.bw --filterRNAstrand forward
bamCoverage -b a.bam -o reverse.bw --filterRNAstrand reverse

# 如果在2.2版本之前：
bamCoverage -b a.bam -o a.fwd.bw --samFlagExclude 16
bamCoverage -b a.bam -o a.rev.bw --samFlagInclude 16

对于strand-specific的双端数据（常用的的d-UTP，--rf型, 1+-,1-+;2++,2--）：

# 得到forward-strand
# exclude reads that are mapped to the reverse strand (16)
$ samtools view -b -f 128 -F 16 a.bam > a.fwd1.bam

# exclude reads that are mapped to the reverse strand (16) and
# first in a pair (64): 64 + 16 = 80
$ samtools view -b -f 80 a.bam > a.fwd2.bam

# combine the temporary files
$ samtools merge -f fwd.bam a.fwd1.bam a.fwd2.bam

# index the filtered BAM file
$ samtools index fwd.bam

# run bamCoverage
$ bamCoverage -b fwd.bam -o a.fwd.bigWig

# remove the temporary files
$ rm a.fwd*.bam


# 得到reverse-strand：
# and are second in a pair (16): 128 + 16 = 144
$ samtools view -b -f 144 a.bam > a.rev1.bam

# include reads that are first in a pair (64), but
# exclude those ones that map to the reverse strand (16)
$ samtools view -b -f 64 -F 16 a.bam > a.rev2.bam

# merge the temporary files
$ samtools merge -f rev.bam a.rev1.bam a.rev2.bam

# index the merged, filtered BAM file
$ samtools index rev.bam

# run bamCoverage
$ bamCoverage -b rev.bam -o a.rev.bw

# remove temporary files
$ rm a.rev*.bam

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