在制备测序文库时，经常会增加PCR的步骤来扩增DNA片段。如何评估PCR的效果和影响，本文主要分享ENCODE中针对ChIP-Seq和ATAC-Seq标准来说明。

ENCODE中主要通过三个参数来反应Library Complexity：PCB1，PBC2和NRF。以下分别介绍各自的定义：

PCR Bottlenecking Coefficient 1 (PBC1)

• PBC1=M1/M_DISTINCT where
  • M1: number of genomic locations where exactly one read maps uniquely
  • M_DISTINCT: number of distinct genomic locations to which some read maps uniquely

PCR Bottlenecking Coefficient 2 (PBC2)

• PBC2= M1/M2 where
  • M1: number of genomic locations where only one read maps uniquely
  • M2: number of genomic locations where two reads map uniquely

Non-Redundant Fraction (NRF) - Number of distinct uniquely mapping reads (i.e. after removing duplicates) / Total number of reads.

如何计算这三个数值呢，在我们拿到比对的结果后（SAM或者BAM文件）

对于single end测序，以align.bam为例：

对于pair-end测序，以align.bam为例：

最后文件中包含7列，分别为：

1）TotalReadPairs

2）DistinctReadPairs

3）OneReadPair

4）TwoReadPairs

5）NRF=Distinct/Total

6）PBC1=OnePair/Distinct

7）PBC2=OnePair/TwoPair

对于ChIP-seq结果解读:

对于ATAC-Seq结果解读:

在制备测序文库时，经常会增加PCR的步骤来扩增DNA片段。如何评估PCR的效果和影响，本文主要分享ENCODE中针对ChIP-Seq和ATAC-Seq标准来说明。

ENCODE中主要通过三个参数来反应Library Complexity：PCB1，PBC2和NRF。以下分别介绍各自的定义：

PCR Bottlenecking Coefficient 1 (PBC1)

• PBC1=M1/M_DISTINCT where
  • M1: number of genomic locations where exactly one read maps uniquely
  • M_DISTINCT: number of distinct genomic locations to which some read maps uniquely

PCR Bottlenecking Coefficient 2 (PBC2)

• PBC2= M1/M2 where
  • M1: number of genomic locations where only one read maps uniquely
  • M2: number of genomic locations where two reads map uniquely

Non-Redundant Fraction (NRF) - Number of distinct uniquely mapping reads (i.e. after removing duplicates) / Total number of reads.

如何计算这三个数值呢，在我们拿到比对的结果后（SAM或者BAM文件）

对于single end测序，以align.bam为例：

对于pair-end测序，以align.bam为例：

最后文件中包含7列，分别为：

1）TotalReadPairs

2）DistinctReadPairs

3）OneReadPair

4）TwoReadPairs

5）NRF=Distinct/Total

6）PBC1=OnePair/Distinct

7）PBC2=OnePair/TwoPair

对于ChIP-seq结果解读:

对于ATAC-Seq结果解读: