# 评估测序文库复杂度 Library Complexity

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ENCODE中主要通过三个参数来反应Library Complexity：PCB1PBC2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.

```bedtools bamtobed -i align.bam | \
awk \'BEGIN{OFS="\t"}{print \$1,\$2,\$3,\$6}\' | \
grep -v \'chrM\' | sort | uniq -c | \
awk \'BEGIN{mt=0;m0=0;m1=0;m2=0} (\$1==1){m1=m1 1} (\$1==2){m2=m2 1} {m0=m0 1} {mt=mt \$1} END{m1_m2=-1.0; if(m2>0) m1_m2=m1/m2; printf "%d\t%d\t%d\t%d\t%f\t%f\t%f\n",mt,m0,m1,m2,m0/mt,m1/m0,m1_m2}\' > pbc_qc.txt```

```bedtools bamtobed -bedpe -i align.bam | \
awk \'BEGIN{OFS="\t"}{print \$1,\$2,\$4,\$6,\$9,\$10}\' | \
grep -v \'chrM\' | sort | uniq -c | \
awk \'BEGIN{mt=0;m0=0;m1=0;m2=0} (\$1==1){m1=m1 1} (\$1==2){m2=m2 1} {m0=m0 1} {mt=mt \$1} END{m1_m2=-1.0; if(m2>0) m1_m2=m1/m2; printf "%d\t%d\t%d\t%d\t%f\t%f\t%f\n",mt,m0,m1,m2,m0/mt,m1/m0,m1_m2}\' > pbc_qc.txt```

1）TotalReadPairs

2）DistinctReadPairs

3）OneReadPair

4）TwoReadPairs

5）NRF=Distinct/Total

6）PBC1=OnePair/Distinct

7）PBC2=OnePair/TwoPair

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