I have a problem with understanding why BWA gives me different results for mapping of single file and multiple files. To be more clear I used bwa aln and samse (commands below) to check list of primers. I have 4 files with primer sequences. The mapping results were checked by samtools flagstat.
bwa aln <reference> <fasta file with starters> > <sai file> bwa samse <reference> <sai file> <fasta file with straters> > <sam file>
At the end I have 4 BAM files from individual mapping and 1 from simultaneously mapping (all starters in the same file -primers merged together to fasta file). The results differ a lot! All of starters are mapped by individual mapping but together only 88%. I am using BWA Version: 0.7.12-r1039.
Can anyone help me with that?
Thanks in advance!