diffrence between number of reads in fastqc reports and collectalignmentsummarymetrics of Picard
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5.6 years ago
kk.mahsa ▴ 140

hi everyone

i have 4 fastq files (two lane correspond to one organism), after filtration of reads, FastQC tell me that total number of reads is 628748302, i mapped them to reference genome and merged resulted two bam file and then sorted it. Now when i run collectalignmentsummarymetrics of Picard to get total and mapped read number, Picard tell me that total number of reads is 628601638. also when i used samtools flagstat, number of total reads counted 629770210, which number is correct?

thanks

Picard FastQC BAM READs • 2.6k views
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