deeptools 提供两个bam转换为bw的命令,分别是 bamCoverage 和 bamCompare 。两者的区别在于 bamCoverage 是对单个bam文件进行转换,而 bamCompare 接受两个bam文件,生成两者信号比值的bw文件。以下是ChIP-seq 数据转换的一个示例用法 -b, --bam : 输入的bam文件 -o :输出的bw文件 -bs, --binSi...
echo "sample name:{wildcards.sample}" > {output} infer_experiment.py -r {input.bed} -i {input.bam} >> {output} 2>&1 """rule bam2bw:input:bam=op.join(base,gse,"results/mapping","{sample}","{sample}.rmdup.bam"),strand=op.join(base,gse,"results/strand_specific","{sample}.st...
bamCompare -b1 treatment.bam -b2 control.bam -o log2ratio.bw \ --scaleFactorsMethod readCount \ --binSize 10 \ --operation log2 \ --pseudocount 1 其中, -b1:处理组的bam文件 -b2:控制组的bam文件 -o:输出的bw文件 --scaleFactorsMethod: Possible choices: readCount, SES, None。用于校正...