Hello everyone,I want to know when we use bwa-sw to alignment,Does its output.sam contain "non-mapping reads"? Because I use default to align 454 against human genomes,output.sam using samtools transfer to bam;and use the command "samtool view f -4 <output.bam>" . It doesn't show any non-mapping reads.
If anyone know the answer,please let me know!!
thanks!!!
Best regard!!
If anyone know the answer,please let me know!!
thanks!!!
Best regard!!