I have a sample's data, using illumina 's Piar End sequencing technology.
RE19E2T40PA_L1_I040.pairPrimer_1.fastq (Read1)
RE19E2T40PA_L1_I040.pairPrimer_2.fastq (Read2)
I have aligned both Read1 and Read2 to hg19 using BWA, and generated three bam file.
RE19E2T40PA_L1_I040.pairPrimer_1.fastq.read1.sorted.bam (Read1's bam file, generated via command :' bwa samse' )
RE19E2T40PA_L1_I040.pairPrimer_1.fastq.read2.sorted.bam (Read2's bam file, generated via command :' bwa samse' )
RE19E2T40PA_L1_I040.pairPrimer_1.fastq.sorted.bam (pair end bam file, generated via command :' bwa sampe' )
Then I using picard to generate alignment statistics.
java -jar /usr/app/picard/picard-tools-1.77/CollectAlignmentSummaryMetrics.jar R=/home/share/hg19/ucsc.hg19.fasta I=RE19E2T40PA_L1_I040.pairPrimer_1.fastq.read1.sorted.bam O=RE19E2T40PA_L1_I040.pairPrimer_1.fastq.read1.sorted.bam.stat
java -jar /usr/app/picard/picard-tools-1.77/CollectAlignmentSummaryMetrics.jar R=/home/share/hg19/ucsc.hg19.fasta I=RE19E2T40PA_L1_I040.pairPrimer_1.fastq.read2.sorted.bam O=RE19E2T40PA_L1_I040.pairPrimer_1.fastq.read2.sorted.bam.stat
java -jar /usr/app/picard/picard-tools-1.77/CollectAlignmentSummaryMetrics.jar R=/home/share/hg19/ucsc.hg19.fasta I=RE19E2T40PA_L1_I040.pairPrimer_1.fastq.sorted.bam O=RE19E2T40PA_L1_I040.pairPrimer_1.fastq.sorted.bam.stat
Look below! The results are contradictory:
Read1's alignment statistic ('RE19E2T40PA_L1_I040.pairPrimer_1.fastq.read1.sorted.bam.stat')
CATEGORY TOTAL_READS PF_READS PCT_PF_READS PF_NOISE_READS PF_READS_ALIGNED PCT_PF_READS_ALIGNED
UNPAIRED 225020 225020 1 0 127242 56.55%
Read2's alignment statistic('RE19E2T40PA_L1_I040.pairPrimer_1.fastq.read2.sorted.bam.stat')
CATEGORY TOTAL_READS PF_READS PCT_PF_READS PF_NOISE_READS PF_READS_ALIGNED PCT_PF_READS_ALIGNED
UNPAIRED 225020 225020 1 0 44101 19.60%
Pair End's alignemnt statistic (RE19E2T40PA_L1_I040.pairPrimer_1.fastq.sorted.bam.stat)
CATEGORY TOTAL_READS PF_READS PCT_PF_READS PF_NOISE_READS PF_READS_ALIGNED PCT_PF_READS_ALIGNED
FIRST_OF_PAIR 225020 225020 1 0 129286 57.46%
SECOND_OF_PAIR 225020 225020 1 0 87054 38.69%
PAIR 450040 450040 1 0 216340 48.07%
Read1 have 127242(56.55%) reads aligned by standalone while 129286(57.46%) reads aligned by Pair Ends.
Read2 have 44101(19.60%) reads alingned by standalone while 87054(38.69%) reads aligned by Pair Ends <--- This is so different, why?