Dear BWA lists, Recently I tried to use BWA mem algorithm for aligning our reads and I found there is some difference between their results. So I have 75bp single end reads, I have reads file from 4 lanes and I did alignment separately and merged later, below are samtools flagstat output for aln and mem, respectively:
mem: samtools flagstat combine_index1.bam 33187055 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 secondary 18543 + 0 supplimentary 0 + 0 duplicates 28739571 + 0 mapped (86.60%:-nan%) 0 + 0 paired in sequencing 0 + 0 read1 0 + 0 read2 0 + 0 properly paired (-nan%:-nan%) 0 + 0 with itself and mate mapped 0 + 0 singletons (-nan%:-nan%) 0 + 0 with mate mapped to a different chr 0 + 0 with mate mapped to a different chr (mapQ>=5) aln: $ samtools flagstat combine_index1.bam 33168512 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 secondary 0 + 0 supplimentary 0 + 0 duplicates 22191474 + 0 mapped (66.91%:-nan%) 0 + 0 paired in sequencing 0 + 0 read1 0 + 0 read2 0 + 0 properly paired (-nan%:-nan%) 0 + 0 with itself and mate mapped 0 + 0 singletons (-nan%:-nan%) 0 + 0 with mate mapped to a different chr 0 + 0 with mate mapped to a different chr (mapQ>=5) my question is that why the total reads number would differ? And also there is large difference between mapped reads count also... is this normal? tools versions: Program: bwa (alignment via Burrows-Wheeler transformation) Version: 0.7.10-r789 Program: samtools (Tools for alignments in the SAM format) Version: 1.1 (using htslib 1.1) Thanks. Daofeng
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