For unmapped reads, I believe
samtools view -f 4 file.bam > unmapped.bam
However, for mapped reads, the command line maybe not work properly unless "no
multiple mapping read in BAM".
samtools view -F 4 file.bam > mapped.sam
I assume samtools does not check whether a read is mapped to multiple
locations. For pair-ended sequencing, the mapping is more complex. In addition
to unmapped reads, a read pair can be uniquely mapped or multiple location.
Likewise, for singleton, one read can be mapped to multiple locations or
uniquely with its mate unapped.
What I want is: extract mapped reads and write them into FASTQ files. For
multiple mapping reads, only write them once. Any advice?
Thank you,
Shanrong
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